Haplotype analysis for Martina’s rice loci
This notebook describes the haplotype analysis of rice loci identified by means of GWAS by Martina Huber, Prof. Ronald Pierink’s group.
library(tidyr)
library(dplyr)##
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library("doBy")##
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## smithslibrary(ggbeeswarm)
library(ggpubr)## Warning: package 'ggpubr' was built under R version 4.0.2library(cowplot)##
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decode <- read.csv("new_haplotypes/accession index_HYDRA-ID_for_Magda.csv")
head(decode)decode <- decode[,c(2:7)]
decode$VCF_better <- gsub("@", ".", decode$VCF_code)
pheno <- read.csv("new_haplotypes/14traits_SI_norm.csv")
# make sure that the column names are the same
colnames(pheno)## [1] "index.pots" "HDRA.ID" "NSFTV.ID"
## [4] "IRGC.ID" "Variety" "Subpop"
## [7] "Shoot.area..cm2." "Hull.area..cm2." "Solidity"
## [10] "Perimeter..cm." "Nr.leaves" "Nr.tillers"
## [13] "Plant.height..cm." "Culm.height..cm." "Leaf.length..cm."
## [16] "DW..g." "Leaf.angle..º." "Tiller.angle..º."
## [19] "Erectness..º." "Droopiness..º." "SUM_rank_traits"
## [22] "SUM_norm_traits" "norm_SI_rank" "SI_rank"colnames(decode)[1] <- "HDRA.ID"
pheno2 <- merge(decode, pheno, id=c("HDRA.ID", "NSFTV.ID", "IRGC.ID"))
head(pheno2)pheno_id <- pheno2$VCF_better
unique(pheno_id)## [1] "NSFTV81.006dfe9b.0" "NSFTV39.014ab0f1.0" "NSFTV132.02cc7c6d.0"
## [4] "NSFTV286.044639de.0" "NSFTV643.0491646d.0" "NSFTV32.068b860d.0"
## [7] "NSFTV358.0764178c.0" "NSFTV275.07dac217.0" "NSFTV269.092f15e7.0"
## [10] "NSFTV256.0be20a08.0" "NSFTV6.0d125c0e.0" "NSFTV324.0defa551.0"
## [13] "NSFTV287.0e787735.0" "NSFTV126.0f6a67da.0" "NSFTV110.11bf5114.0"
## [16] "NSFTV355.122a975b.0" "NSFTV150.128dd425.0" "NSFTV72.12d82364.0"
## [19] "NSFTV311.137628a5.0" "NSFTV235.13ae4f27.0" "NSFTV216.149fb038.0"
## [22] "NSFTV364.14e43b02.0" "NSFTV323.1510e4aa.0" "NSFTV277.1516d75f.0"
## [25] "NSFTV177.15e6c437.0" "NSFTV105.16463092.0" "NSFTV278.17627a92.0"
## [28] "NSFTV145.17c4070a.0" "NSFTV391.180a155f.0" "NSFTV253.1911c363.0"
## [31] "NSFTV163.192e24ab.0" "NSFTV228.195567bf.0" "NSFTV27.1956dd3f.0"
## [34] "NSFTV219.199f4455.0" "NSFTV138.1a946dc6.0" "NSFTV133.1a95985b.0"
## [37] "NSFTV65.1ab838a2.0" "NSFTV25.1ce7093b.0" "NSFTV335.1e26852c.0"
## [40] "NSFTV328.1e4f3933.0" "NSFTV396.1eb5d579.0" "NSFTV100.1f10be3d.0"
## [43] "NSFTV321.1f6f13c3.0" "NSFTV394.1f856ac1.0" "NSFTV94.20a4c97d.0"
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## [325] "#N/A"Locus 1 Os03g0843700 RAP2
list.files(pattern=".csv")## [1] "L1_Haplotype_Os03g0841800_RAP2_gene_and_pheno.csv"
## [2] "L1_Haplotype_Os03g0843700_RAP2_gene.csv"
## [3] "L1_Haplotype_Os03g0845000_RAP2_gene.csv"
## [4] "L1_Haplotype_Os03g0845700_RAP2_gene.csv"
## [5] "L1_Haplotype_Os03g0845800_RAP2_gene.csv"
## [6] "L1_Haplotype_Os03g0848700_RAP2_gene.csv"
## [7] "L1_Haplotype_Os03g62400_gene_and_pheno.csv"
## [8] "L2_Haplotype_Os05g0420500_RAP2_gene.csv"
## [9] "L2_Haplotype_Os05g0420600_RAP2_gene.csv"
## [10] "L2_Haplotype_Os05g0420900_RAP2_gene.csv"
## [11] "L3_Haplotype_Os06g0346300_RAP2_gene.csv"
## [12] "L4_Haplotype_Os07g0623200_RAP2_gene.csv"
## [13] "L4_Haplotype_Os07g0623501_RAP2_gene.csv"
## [14] "L4_Haplotype_Os07g0623600_RAP2_gene.csv"
## [15] "L4_Haplotype_Os07g43040_gene.csv"
## [16] "L6_Haplotype_Os11g0216000_RAB2_gene.csv"
## [17] "Locus_1_final_file.csv"
## [18] "Locus_2_final_file.csv"
## [19] "Locus_3_final_file.csv"
## [20] "Locus_4_final_file.csv"
## [21] "Locus_6_final_file.csv"temp <- read.csv("L1_Haplotype_Os03g0843700_RAP2_gene.csv")
head(temp)haplotype2 <- temp[,c(1, 14)]
ultimate2 <- merge(pheno2, haplotype2, by=c("VCF_better"))
head(ultimate2)unique(ultimate2$haplotype)## [1] "AAAAAAA" "AAAAATT" "TAAAATA" "AAAAATA" "ATATTTA"# let's see which haplotype is most popular among accessions:
ultimate2 %>% group_by(haplotype) %>%
tally()In this case - we have 6 original haplotypes - but only 1 of them is represented by 3 or more accessions
ultimate2$haplotype <- gsub("AAAAATT", "hap01", ultimate2$haplotype)
ultimate2$haplotype <- gsub("AAAAAAA", "hap02", ultimate2$haplotype)
ultimate2$haplotype <- gsub("AAAAATA", "hap03", ultimate2$haplotype)
ultimate2$haplotype <- gsub("TAAAATA", "hap04", ultimate2$haplotype)
ultimate2$haplotype <- gsub("ATATTTA", "hap05", ultimate2$haplotype)
ultimate2$haplotype <- factor(ultimate2$haplotype, levels = c("hap01", "hap02", "hap03", "hap04", "hap05"))
colnames(ultimate2)## [1] "VCF_better" "HDRA.ID" "NSFTV.ID"
## [4] "IRGC.ID" "Subpop" "Accession.Name"
## [7] "VCF_code" "index.pots" "Variety"
## [10] "Shoot.area..cm2." "Hull.area..cm2." "Solidity"
## [13] "Perimeter..cm." "Nr.leaves" "Nr.tillers"
## [16] "Plant.height..cm." "Culm.height..cm." "Leaf.length..cm."
## [19] "DW..g." "Leaf.angle..º." "Tiller.angle..º."
## [22] "Erectness..º." "Droopiness..º." "SUM_rank_traits"
## [25] "SUM_norm_traits" "norm_SI_rank" "SI_rank"
## [28] "haplotype"OK - now let’s graph them:
Output <- TukeyHSD(aov(aov(Shoot.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Shoot.area..cm2., colour = haplotype))
my_box_plot <- my_box_plot + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot <- my_box_plot + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot <- my_box_plot + theme(legend.position = "none")
my_box_plot <- my_box_plot + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot <- my_box_plot + xlab("") + ylab(expression(paste("Shoot area (", cm^2, ")", sep = "")))
my_box_plot <- my_box_plot + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot <- my_box_plot + stat_pvalue_manual(test, label = "Tukey", y.position = 950)
my_box_plot
Output <- TukeyHSD(aov(aov(Hull.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot2 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Hull.area..cm2., colour = haplotype))
my_box_plot2 <- my_box_plot2 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot2 <- my_box_plot2 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot2 <- my_box_plot2 + theme(legend.position = "none")
my_box_plot2 <- my_box_plot2 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot2 <- my_box_plot2 + xlab("") + ylab(expression(paste("Hull area (", cm^2, ")", sep = "")))
my_box_plot2 <- my_box_plot2 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot2 <- my_box_plot2 + stat_pvalue_manual(test, label = "Tukey", y.position = 6000)
my_box_plot2
Output <- TukeyHSD(aov(aov(Solidity ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot3 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Solidity, colour = haplotype))
my_box_plot3 <- my_box_plot3 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot3 <- my_box_plot3 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot3 <- my_box_plot3 + theme(legend.position = "none")
my_box_plot3 <- my_box_plot3 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot3 <- my_box_plot3 + xlab("") + ylab("Solidity (a.u.)")
my_box_plot3 <- my_box_plot3 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot3 <- my_box_plot3 + stat_pvalue_manual(test, label = "Tukey", y.position = 0.21)
my_box_plot3
Output <- TukeyHSD(aov(aov(Perimeter..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot4 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Perimeter..cm., colour = haplotype))
my_box_plot4 <- my_box_plot4 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot4 <- my_box_plot4 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot4 <- my_box_plot4 + theme(legend.position = "none")
my_box_plot4 <- my_box_plot4 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot4 <- my_box_plot4 + xlab("") + ylab("Perimeter (cm)")
my_box_plot4 <- my_box_plot4 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot4 <- my_box_plot4 + stat_pvalue_manual(test, label = "Tukey", y.position = 2500)
my_box_plot4
Output <- TukeyHSD(aov(aov(Nr.leaves ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot5 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.leaves, colour = haplotype))
my_box_plot5 <- my_box_plot5 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot5 <- my_box_plot5 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot5 <- my_box_plot5 + theme(legend.position = "none")
my_box_plot5 <- my_box_plot5 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot5 <- my_box_plot5 + xlab("") + ylab("Leaf number")
my_box_plot5 <- my_box_plot5 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot5 <- my_box_plot5 + stat_pvalue_manual(test, label = "Tukey", y.position = 55)
my_box_plot5
Output <- TukeyHSD(aov(aov(Nr.tillers ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot6 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.tillers, colour = haplotype))
my_box_plot6 <- my_box_plot6 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot6 <- my_box_plot6 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot6 <- my_box_plot6 + theme(legend.position = "none")
my_box_plot6 <- my_box_plot6 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot6 <- my_box_plot6 + xlab("") + ylab("Tiller number")
my_box_plot6 <- my_box_plot6 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot6 <- my_box_plot6 + stat_pvalue_manual(test, label = "Tukey", y.position = 17)
my_box_plot6
Output <- TukeyHSD(aov(aov(Plant.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot7 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Plant.height..cm., colour = haplotype))
my_box_plot7 <- my_box_plot7 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot7 <- my_box_plot7 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot7 <- my_box_plot7 + theme(legend.position = "none")
my_box_plot7 <- my_box_plot7 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot7 <- my_box_plot7 + xlab("") + ylab("Plant height (cm)")
my_box_plot7 <- my_box_plot7 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot7 <- my_box_plot7 + stat_pvalue_manual(test, label = "Tukey", y.position = 95)
my_box_plot7
Output <- TukeyHSD(aov(aov(Culm.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot8 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Culm.height..cm., colour = haplotype))
my_box_plot8 <- my_box_plot8 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot8 <- my_box_plot8 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot8 <- my_box_plot8 + theme(legend.position = "none")
my_box_plot8 <- my_box_plot8 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot8 <- my_box_plot8 + xlab("") + ylab("Culm height (cm)")
my_box_plot8 <- my_box_plot8 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot8 <- my_box_plot8 + stat_pvalue_manual(test, label = "Tukey", y.position = 35)
my_box_plot8
Output <- TukeyHSD(aov(aov(Leaf.length..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot9 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.length..cm., colour = haplotype))
my_box_plot9 <- my_box_plot9 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot9 <- my_box_plot9 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot9 <- my_box_plot9 + theme(legend.position = "none")
my_box_plot9 <- my_box_plot9 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot9 <- my_box_plot9 + xlab("") + ylab("Leaf length (cm)")
my_box_plot9 <- my_box_plot9 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot9 <- my_box_plot9 + stat_pvalue_manual(test, label = "Tukey", y.position = 65)
my_box_plot9
Output <- TukeyHSD(aov(aov(DW..g. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot10 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = DW..g., colour = haplotype))
my_box_plot10 <- my_box_plot10 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot10 <- my_box_plot10 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot10 <- my_box_plot10 + theme(legend.position = "none")
my_box_plot10 <- my_box_plot10 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot10 <- my_box_plot10 + xlab("") + ylab("Dry weight (g)")
my_box_plot10 <- my_box_plot10 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot10 <- my_box_plot10 + stat_pvalue_manual(test, label = "Tukey", y.position = 4)
my_box_plot10
Output <- TukeyHSD(aov(aov(Leaf.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot11 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.angle..º., colour = haplotype))
my_box_plot11 <- my_box_plot11 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot11 <- my_box_plot11 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot11 <- my_box_plot11 + theme(legend.position = "none")
my_box_plot11 <- my_box_plot11 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot11 <- my_box_plot11 + xlab("") + ylab("Leaf angle (º)")
my_box_plot11 <- my_box_plot11 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot11 <- my_box_plot11 + stat_pvalue_manual(test, label = "Tukey", y.position = 65)
my_box_plot11
Output <- TukeyHSD(aov(aov(Tiller.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot12 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Tiller.angle..º., colour = haplotype))
my_box_plot12 <- my_box_plot12 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot12 <- my_box_plot12 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot12 <- my_box_plot12 + theme(legend.position = "none")
my_box_plot12 <- my_box_plot12 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot12 <- my_box_plot12 + xlab("") + ylab("Tiller angle (º)")
my_box_plot12 <- my_box_plot12 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot12 <- my_box_plot12 + stat_pvalue_manual(test, label = "Tukey", y.position = 37)
my_box_plot12
Output <- TukeyHSD(aov(aov(Erectness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot13 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Erectness..º., colour = haplotype))
my_box_plot13 <- my_box_plot13 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot13 <- my_box_plot13 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot13 <- my_box_plot13 + theme(legend.position = "none")
my_box_plot13 <- my_box_plot13 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot13 <- my_box_plot13 + xlab("") + ylab("Erectness (º)")
my_box_plot13 <- my_box_plot13 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot13 <- my_box_plot13 + stat_pvalue_manual(test, label = "Tukey", y.position = 165)
my_box_plot13
Output <- TukeyHSD(aov(aov(Droopiness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot14 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Droopiness..º., colour = haplotype))
my_box_plot14 <- my_box_plot14 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot14 <- my_box_plot14 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot14 <- my_box_plot14 + theme(legend.position = "none")
my_box_plot14 <- my_box_plot14 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot14 <- my_box_plot14 + xlab("") + ylab("Droopiness (º)")
my_box_plot14 <- my_box_plot14 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot14 <- my_box_plot14 + stat_pvalue_manual(test, label = "Tukey", y.position = 170)
my_box_plot14
pdf("Locus_01_Haplotypes_Os03g0843700_RAP2_NEW.pdf", height = 30, width = 12)
plot_grid(my_box_plot, my_box_plot2, my_box_plot3, my_box_plot4, my_box_plot5, my_box_plot6, my_box_plot7, my_box_plot8, my_box_plot9, my_box_plot10, my_box_plot11, my_box_plot12, my_box_plot13, my_box_plot14,
ncol=2,
align = "hv", labels=c("AUTO"),
label_size = 24)
dev.off()## quartz_off_screen
## 2Locus 1 Os03g0845000 RAP2
list.files(pattern=".csv")## [1] "L1_Haplotype_Os03g0841800_RAP2_gene_and_pheno.csv"
## [2] "L1_Haplotype_Os03g0843700_RAP2_gene.csv"
## [3] "L1_Haplotype_Os03g0845000_RAP2_gene.csv"
## [4] "L1_Haplotype_Os03g0845700_RAP2_gene.csv"
## [5] "L1_Haplotype_Os03g0845800_RAP2_gene.csv"
## [6] "L1_Haplotype_Os03g0848700_RAP2_gene.csv"
## [7] "L1_Haplotype_Os03g62400_gene_and_pheno.csv"
## [8] "L2_Haplotype_Os05g0420500_RAP2_gene.csv"
## [9] "L2_Haplotype_Os05g0420600_RAP2_gene.csv"
## [10] "L2_Haplotype_Os05g0420900_RAP2_gene.csv"
## [11] "L3_Haplotype_Os06g0346300_RAP2_gene.csv"
## [12] "L4_Haplotype_Os07g0623200_RAP2_gene.csv"
## [13] "L4_Haplotype_Os07g0623501_RAP2_gene.csv"
## [14] "L4_Haplotype_Os07g0623600_RAP2_gene.csv"
## [15] "L4_Haplotype_Os07g43040_gene.csv"
## [16] "L6_Haplotype_Os11g0216000_RAB2_gene.csv"
## [17] "Locus_1_final_file.csv"
## [18] "Locus_2_final_file.csv"
## [19] "Locus_3_final_file.csv"
## [20] "Locus_4_final_file.csv"
## [21] "Locus_6_final_file.csv"temp <- read.csv("L1_Haplotype_Os03g0845000_RAP2_gene.csv")
head(temp)haplotype2 <- temp[,c(1, 14)]
ultimate2 <- merge(pheno2, haplotype2, by=c("VCF_better"))
head(ultimate2)unique(ultimate2$haplotype)## [1] "AA" "TA" "TT"# let's see which haplotype is most popular among accessions:
ultimate2 %>% group_by(haplotype) %>%
tally()ultimate2$haplotype <- gsub("TA", "hap01", ultimate2$haplotype)
ultimate2$haplotype <- gsub("AA", "hap02", ultimate2$haplotype)
ultimate2$haplotype <- gsub("TT", "hap03", ultimate2$haplotype)
ultimate2$haplotype <- factor(ultimate2$haplotype, levels = c("hap01", "hap02", "hap03"))
colnames(ultimate2)## [1] "VCF_better" "HDRA.ID" "NSFTV.ID"
## [4] "IRGC.ID" "Subpop" "Accession.Name"
## [7] "VCF_code" "index.pots" "Variety"
## [10] "Shoot.area..cm2." "Hull.area..cm2." "Solidity"
## [13] "Perimeter..cm." "Nr.leaves" "Nr.tillers"
## [16] "Plant.height..cm." "Culm.height..cm." "Leaf.length..cm."
## [19] "DW..g." "Leaf.angle..º." "Tiller.angle..º."
## [22] "Erectness..º." "Droopiness..º." "SUM_rank_traits"
## [25] "SUM_norm_traits" "norm_SI_rank" "SI_rank"
## [28] "haplotype"OK - now let’s graph them:
Output <- TukeyHSD(aov(aov(Shoot.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Shoot.area..cm2., colour = haplotype))
my_box_plot <- my_box_plot + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot <- my_box_plot + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot <- my_box_plot + theme(legend.position = "none")
my_box_plot <- my_box_plot + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot <- my_box_plot + xlab("") + ylab(expression(paste("Shoot area (", cm^2, ")", sep = "")))
my_box_plot <- my_box_plot + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot <- my_box_plot + stat_pvalue_manual(test, label = "Tukey", y.position = 950)
my_box_plot
Output <- TukeyHSD(aov(aov(Hull.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot2 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Hull.area..cm2., colour = haplotype))
my_box_plot2 <- my_box_plot2 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot2 <- my_box_plot2 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot2 <- my_box_plot2 + theme(legend.position = "none")
my_box_plot2 <- my_box_plot2 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot2 <- my_box_plot2 + xlab("") + ylab(expression(paste("Hull area (", cm^2, ")", sep = "")))
my_box_plot2 <- my_box_plot2 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot2 <- my_box_plot2 + stat_pvalue_manual(test, label = "Tukey", y.position = 6000)
my_box_plot2
Output <- TukeyHSD(aov(aov(Solidity ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot3 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Solidity, colour = haplotype))
my_box_plot3 <- my_box_plot3 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot3 <- my_box_plot3 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot3 <- my_box_plot3 + theme(legend.position = "none")
my_box_plot3 <- my_box_plot3 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot3 <- my_box_plot3 + xlab("") + ylab("Solidity (a.u.)")
my_box_plot3 <- my_box_plot3 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot3 <- my_box_plot3 + stat_pvalue_manual(test, label = "Tukey", y.position = 0.21)
my_box_plot3
Output <- TukeyHSD(aov(aov(Perimeter..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot4 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Perimeter..cm., colour = haplotype))
my_box_plot4 <- my_box_plot4 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot4 <- my_box_plot4 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot4 <- my_box_plot4 + theme(legend.position = "none")
my_box_plot4 <- my_box_plot4 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot4 <- my_box_plot4 + xlab("") + ylab("Perimeter (cm)")
my_box_plot4 <- my_box_plot4 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot4 <- my_box_plot4 + stat_pvalue_manual(test, label = "Tukey", y.position = 2500)
my_box_plot4
Output <- TukeyHSD(aov(aov(Nr.leaves ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot5 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.leaves, colour = haplotype))
my_box_plot5 <- my_box_plot5 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot5 <- my_box_plot5 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot5 <- my_box_plot5 + theme(legend.position = "none")
my_box_plot5 <- my_box_plot5 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot5 <- my_box_plot5 + xlab("") + ylab("Leaf number")
my_box_plot5 <- my_box_plot5 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot5 <- my_box_plot5 + stat_pvalue_manual(test, label = "Tukey", y.position = 55)
my_box_plot5
Output <- TukeyHSD(aov(aov(Nr.tillers ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot6 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.tillers, colour = haplotype))
my_box_plot6 <- my_box_plot6 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot6 <- my_box_plot6 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot6 <- my_box_plot6 + theme(legend.position = "none")
my_box_plot6 <- my_box_plot6 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot6 <- my_box_plot6 + xlab("") + ylab("Tiller number")
my_box_plot6 <- my_box_plot6 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot6 <- my_box_plot6 + stat_pvalue_manual(test, label = "Tukey", y.position = 17)
my_box_plot6
Output <- TukeyHSD(aov(aov(Plant.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot7 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Plant.height..cm., colour = haplotype))
my_box_plot7 <- my_box_plot7 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot7 <- my_box_plot7 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot7 <- my_box_plot7 + theme(legend.position = "none")
my_box_plot7 <- my_box_plot7 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot7 <- my_box_plot7 + xlab("") + ylab("Plant height (cm)")
my_box_plot7 <- my_box_plot7 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot7 <- my_box_plot7 + stat_pvalue_manual(test, label = "Tukey", y.position = 95)
my_box_plot7
Output <- TukeyHSD(aov(aov(Culm.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot8 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Culm.height..cm., colour = haplotype))
my_box_plot8 <- my_box_plot8 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot8 <- my_box_plot8 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot8 <- my_box_plot8 + theme(legend.position = "none")
my_box_plot8 <- my_box_plot8 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot8 <- my_box_plot8 + xlab("") + ylab("Culm height (cm)")
my_box_plot8 <- my_box_plot8 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot8 <- my_box_plot8 + stat_pvalue_manual(test, label = "Tukey", y.position = 35)
my_box_plot8
Output <- TukeyHSD(aov(aov(Leaf.length..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot9 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.length..cm., colour = haplotype))
my_box_plot9 <- my_box_plot9 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot9 <- my_box_plot9 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot9 <- my_box_plot9 + theme(legend.position = "none")
my_box_plot9 <- my_box_plot9 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot9 <- my_box_plot9 + xlab("") + ylab("Leaf length (cm)")
my_box_plot9 <- my_box_plot9 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot9 <- my_box_plot9 + stat_pvalue_manual(test, label = "Tukey", y.position = 65)
my_box_plot9
Output <- TukeyHSD(aov(aov(DW..g. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot10 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = DW..g., colour = haplotype))
my_box_plot10 <- my_box_plot10 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot10 <- my_box_plot10 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot10 <- my_box_plot10 + theme(legend.position = "none")
my_box_plot10 <- my_box_plot10 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot10 <- my_box_plot10 + xlab("") + ylab("Dry weight (g)")
my_box_plot10 <- my_box_plot10 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot10 <- my_box_plot10 + stat_pvalue_manual(test, label = "Tukey", y.position = 4)
my_box_plot10
Output <- TukeyHSD(aov(aov(Leaf.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot11 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.angle..º., colour = haplotype))
my_box_plot11 <- my_box_plot11 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot11 <- my_box_plot11 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot11 <- my_box_plot11 + theme(legend.position = "none")
my_box_plot11 <- my_box_plot11 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot11 <- my_box_plot11 + xlab("") + ylab("Leaf angle (º)")
my_box_plot11 <- my_box_plot11 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot11 <- my_box_plot11 + stat_pvalue_manual(test, label = "Tukey", y.position = 65)
my_box_plot11
Output <- TukeyHSD(aov(aov(Tiller.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot12 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Tiller.angle..º., colour = haplotype))
my_box_plot12 <- my_box_plot12 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot12 <- my_box_plot12 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot12 <- my_box_plot12 + theme(legend.position = "none")
my_box_plot12 <- my_box_plot12 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot12 <- my_box_plot12 + xlab("") + ylab("Tiller angle (º)")
my_box_plot12 <- my_box_plot12 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot12 <- my_box_plot12 + stat_pvalue_manual(test, label = "Tukey", y.position = 37)
my_box_plot12
Output <- TukeyHSD(aov(aov(Erectness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot13 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Erectness..º., colour = haplotype))
my_box_plot13 <- my_box_plot13 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot13 <- my_box_plot13 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot13 <- my_box_plot13 + theme(legend.position = "none")
my_box_plot13 <- my_box_plot13 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot13 <- my_box_plot13 + xlab("") + ylab("Erectness (º)")
my_box_plot13 <- my_box_plot13 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot13 <- my_box_plot13 + stat_pvalue_manual(test, label = "Tukey", y.position = 165)
my_box_plot13
Output <- TukeyHSD(aov(aov(Droopiness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot14 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Droopiness..º., colour = haplotype))
my_box_plot14 <- my_box_plot14 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot14 <- my_box_plot14 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot14 <- my_box_plot14 + theme(legend.position = "none")
my_box_plot14 <- my_box_plot14 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot14 <- my_box_plot14 + xlab("") + ylab("Droopiness (º)")
my_box_plot14 <- my_box_plot14 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot14 <- my_box_plot14 + stat_pvalue_manual(test, label = "Tukey", y.position = 170)
my_box_plot14
pdf("Locus_01_Haplotypes_Os03g0845000_RAP2_NEW.pdf", height = 30, width = 12)
plot_grid(my_box_plot, my_box_plot2, my_box_plot3, my_box_plot4, my_box_plot5, my_box_plot6, my_box_plot7, my_box_plot8, my_box_plot9, my_box_plot10, my_box_plot11, my_box_plot12, my_box_plot13, my_box_plot14,
ncol=2,
align = "hv", labels=c("AUTO"),
label_size = 24)
dev.off()## quartz_off_screen
## 2Locus 1 Os03g0845700 RAP2
list.files(pattern=".csv")## [1] "L1_Haplotype_Os03g0841800_RAP2_gene_and_pheno.csv"
## [2] "L1_Haplotype_Os03g0843700_RAP2_gene.csv"
## [3] "L1_Haplotype_Os03g0845000_RAP2_gene.csv"
## [4] "L1_Haplotype_Os03g0845700_RAP2_gene.csv"
## [5] "L1_Haplotype_Os03g0845800_RAP2_gene.csv"
## [6] "L1_Haplotype_Os03g0848700_RAP2_gene.csv"
## [7] "L1_Haplotype_Os03g62400_gene_and_pheno.csv"
## [8] "L2_Haplotype_Os05g0420500_RAP2_gene.csv"
## [9] "L2_Haplotype_Os05g0420600_RAP2_gene.csv"
## [10] "L2_Haplotype_Os05g0420900_RAP2_gene.csv"
## [11] "L3_Haplotype_Os06g0346300_RAP2_gene.csv"
## [12] "L4_Haplotype_Os07g0623200_RAP2_gene.csv"
## [13] "L4_Haplotype_Os07g0623501_RAP2_gene.csv"
## [14] "L4_Haplotype_Os07g0623600_RAP2_gene.csv"
## [15] "L4_Haplotype_Os07g43040_gene.csv"
## [16] "L6_Haplotype_Os11g0216000_RAB2_gene.csv"
## [17] "Locus_1_final_file.csv"
## [18] "Locus_2_final_file.csv"
## [19] "Locus_3_final_file.csv"
## [20] "Locus_4_final_file.csv"
## [21] "Locus_6_final_file.csv"temp <- read.csv("L1_Haplotype_Os03g0845700_RAP2_gene.csv")
head(temp)haplotype2 <- temp[,c(1, 14)]
ultimate2 <- merge(pheno2, haplotype2, by=c("VCF_better"))
head(ultimate2)unique(ultimate2$haplotype)## [1] "A" "T"# let's see which haplotype is most popular among accessions:
ultimate2 %>% group_by(haplotype) %>%
tally()ultimate2$haplotype <- gsub("T", "hap01", ultimate2$haplotype)
ultimate2$haplotype <- gsub("A", "hap02", ultimate2$haplotype)
ultimate2$haplotype <- factor(ultimate2$haplotype, levels = c("hap01", "hap02"))
colnames(ultimate2)## [1] "VCF_better" "HDRA.ID" "NSFTV.ID"
## [4] "IRGC.ID" "Subpop" "Accession.Name"
## [7] "VCF_code" "index.pots" "Variety"
## [10] "Shoot.area..cm2." "Hull.area..cm2." "Solidity"
## [13] "Perimeter..cm." "Nr.leaves" "Nr.tillers"
## [16] "Plant.height..cm." "Culm.height..cm." "Leaf.length..cm."
## [19] "DW..g." "Leaf.angle..º." "Tiller.angle..º."
## [22] "Erectness..º." "Droopiness..º." "SUM_rank_traits"
## [25] "SUM_norm_traits" "norm_SI_rank" "SI_rank"
## [28] "haplotype"OK - now let’s graph them:
Output <- TukeyHSD(aov(aov(Shoot.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 7.428502e-13test2 <- test[c(1,3),]
my_box_plot <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Shoot.area..cm2., colour = haplotype))
my_box_plot <- my_box_plot + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot <- my_box_plot + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot <- my_box_plot + theme(legend.position = "none")
my_box_plot <- my_box_plot + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot <- my_box_plot + xlab("") + ylab(expression(paste("Shoot area (", cm^2, ")", sep = "")))
my_box_plot <- my_box_plot + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot <- my_box_plot + stat_pvalue_manual(test2, label = "Tukey", y.position = 950)
my_box_plot
Output <- TukeyHSD(aov(aov(Hull.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 6.97653e-12test2 <- test[c(1,3),]
my_box_plot2 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Hull.area..cm2., colour = haplotype))
my_box_plot2 <- my_box_plot2 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot2 <- my_box_plot2 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot2 <- my_box_plot2 + theme(legend.position = "none")
my_box_plot2 <- my_box_plot2 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot2 <- my_box_plot2 + xlab("") + ylab(expression(paste("Hull area (", cm^2, ")", sep = "")))
my_box_plot2 <- my_box_plot2 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot2 <- my_box_plot2 + stat_pvalue_manual(test2, label = "Tukey", y.position = 6000)
my_box_plot2
Output <- TukeyHSD(aov(aov(Solidity ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 8.019962e-11test2 <- test[c(1,3),]
my_box_plot3 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Solidity, colour = haplotype))
my_box_plot3 <- my_box_plot3 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot3 <- my_box_plot3 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot3 <- my_box_plot3 + theme(legend.position = "none")
my_box_plot3 <- my_box_plot3 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot3 <- my_box_plot3 + xlab("") + ylab("Solidity (a.u.)")
my_box_plot3 <- my_box_plot3 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot3 <- my_box_plot3 + stat_pvalue_manual(test2, label = "Tukey", y.position = 0.21)
my_box_plot3
Output <- TukeyHSD(aov(aov(Perimeter..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 7.610579e-13my_box_plot4 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Perimeter..cm., colour = haplotype))
my_box_plot4 <- my_box_plot4 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot4 <- my_box_plot4 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot4 <- my_box_plot4 + theme(legend.position = "none")
my_box_plot4 <- my_box_plot4 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot4 <- my_box_plot4 + xlab("") + ylab("Perimeter (cm)")
my_box_plot4 <- my_box_plot4 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot4 <- my_box_plot4 + stat_pvalue_manual(test2, label = "Tukey", y.position = 2500)
my_box_plot4
Output <- TukeyHSD(aov(aov(Nr.leaves ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 7.456258e-13my_box_plot5 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.leaves, colour = haplotype))
my_box_plot5 <- my_box_plot5 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot5 <- my_box_plot5 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot5 <- my_box_plot5 + theme(legend.position = "none")
my_box_plot5 <- my_box_plot5 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot5 <- my_box_plot5 + xlab("") + ylab("Leaf number")
my_box_plot5 <- my_box_plot5 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot5 <- my_box_plot5 + stat_pvalue_manual(test2, label = "Tukey", y.position = 55)
my_box_plot5
Output <- TukeyHSD(aov(aov(Nr.tillers ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 7.444045e-13my_box_plot6 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.tillers, colour = haplotype))
my_box_plot6 <- my_box_plot6 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot6 <- my_box_plot6 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot6 <- my_box_plot6 + theme(legend.position = "none")
my_box_plot6 <- my_box_plot6 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot6 <- my_box_plot6 + xlab("") + ylab("Tiller number")
my_box_plot6 <- my_box_plot6 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot6 <- my_box_plot6 + stat_pvalue_manual(test2, label = "Tukey", y.position = 17)
my_box_plot6
Output <- TukeyHSD(aov(aov(Plant.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0.1882969test3 <- test2
test3$Tukey <- gsub("b", "a", test3$Tukey)
my_box_plot7 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Plant.height..cm., colour = haplotype))
my_box_plot7 <- my_box_plot7 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot7 <- my_box_plot7 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot7 <- my_box_plot7 + theme(legend.position = "none")
my_box_plot7 <- my_box_plot7 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot7 <- my_box_plot7 + xlab("") + ylab("Plant height (cm)")
my_box_plot7 <- my_box_plot7 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot7 <- my_box_plot7 + stat_pvalue_manual(test3, label = "Tukey", y.position = 95)
my_box_plot7
Output <- TukeyHSD(aov(aov(Culm.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0.01431405my_box_plot8 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Culm.height..cm., colour = haplotype))
my_box_plot8 <- my_box_plot8 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot8 <- my_box_plot8 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot8 <- my_box_plot8 + theme(legend.position = "none")
my_box_plot8 <- my_box_plot8 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot8 <- my_box_plot8 + xlab("") + ylab("Culm height (cm)")
my_box_plot8 <- my_box_plot8 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot8 <- my_box_plot8 + stat_pvalue_manual(test2, label = "Tukey", y.position = 35)
my_box_plot8
Output <- TukeyHSD(aov(aov(Leaf.length..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0.009384355my_box_plot9 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.length..cm., colour = haplotype))
my_box_plot9 <- my_box_plot9 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot9 <- my_box_plot9 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot9 <- my_box_plot9 + theme(legend.position = "none")
my_box_plot9 <- my_box_plot9 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot9 <- my_box_plot9 + xlab("") + ylab("Leaf length (cm)")
my_box_plot9 <- my_box_plot9 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot9 <- my_box_plot9 + stat_pvalue_manual(test2, label = "Tukey", y.position = 65)
my_box_plot9
Output <- TukeyHSD(aov(aov(DW..g. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 7.456258e-13my_box_plot10 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = DW..g., colour = haplotype))
my_box_plot10 <- my_box_plot10 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot10 <- my_box_plot10 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot10 <- my_box_plot10 + theme(legend.position = "none")
my_box_plot10 <- my_box_plot10 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot10 <- my_box_plot10 + xlab("") + ylab("Dry weight (g)")
my_box_plot10 <- my_box_plot10 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot10 <- my_box_plot10 + stat_pvalue_manual(test2, label = "Tukey", y.position = 4)
my_box_plot10
Output <- TukeyHSD(aov(aov(Leaf.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0.02075252my_box_plot11 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.angle..º., colour = haplotype))
my_box_plot11 <- my_box_plot11 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot11 <- my_box_plot11 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot11 <- my_box_plot11 + theme(legend.position = "none")
my_box_plot11 <- my_box_plot11 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot11 <- my_box_plot11 + xlab("") + ylab("Leaf angle (º)")
my_box_plot11 <- my_box_plot11 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot11 <- my_box_plot11 + stat_pvalue_manual(test2, label = "Tukey", y.position = 65)
my_box_plot11
Output <- TukeyHSD(aov(aov(Tiller.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 1.198577e-06my_box_plot12 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Tiller.angle..º., colour = haplotype))
my_box_plot12 <- my_box_plot12 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot12 <- my_box_plot12 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot12 <- my_box_plot12 + theme(legend.position = "none")
my_box_plot12 <- my_box_plot12 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot12 <- my_box_plot12 + xlab("") + ylab("Tiller angle (º)")
my_box_plot12 <- my_box_plot12 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot12 <- my_box_plot12 + stat_pvalue_manual(test2, label = "Tukey", y.position = 37)
my_box_plot12
Output <- TukeyHSD(aov(aov(Erectness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 4.694578e-12my_box_plot13 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Erectness..º., colour = haplotype))
my_box_plot13 <- my_box_plot13 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot13 <- my_box_plot13 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot13 <- my_box_plot13 + theme(legend.position = "none")
my_box_plot13 <- my_box_plot13 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot13 <- my_box_plot13 + xlab("") + ylab("Erectness (º)")
my_box_plot13 <- my_box_plot13 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot13 <- my_box_plot13 + stat_pvalue_manual(test2, label = "Tukey", y.position = 165)
my_box_plot13
Output <- TukeyHSD(aov(aov(Droopiness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 4.694578e-12my_box_plot14 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Droopiness..º., colour = haplotype))
my_box_plot14 <- my_box_plot14 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot14 <- my_box_plot14 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot14 <- my_box_plot14 + theme(legend.position = "none")
my_box_plot14 <- my_box_plot14 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot14 <- my_box_plot14 + xlab("") + ylab("Droopiness (º)")
my_box_plot14 <- my_box_plot14 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot14 <- my_box_plot14 + stat_pvalue_manual(test2, label = "Tukey", y.position = 170)
my_box_plot14
pdf("Locus_01_Haplotypes_Os03g0845700_RAP2_NEW.pdf", height = 30, width = 12)
plot_grid(my_box_plot, my_box_plot2, my_box_plot3, my_box_plot4, my_box_plot5, my_box_plot6,
my_box_plot7, my_box_plot8, my_box_plot9, my_box_plot10, my_box_plot11, my_box_plot12,
my_box_plot13, my_box_plot14,
ncol=2,
align = "hv", labels=c("AUTO"),
label_size = 24)
dev.off()## quartz_off_screen
## 2Locus 2 Os5g0420600
list.files(pattern=".csv")## [1] "L1_Haplotype_Os03g0841800_RAP2_gene_and_pheno.csv"
## [2] "L1_Haplotype_Os03g0843700_RAP2_gene.csv"
## [3] "L1_Haplotype_Os03g0845000_RAP2_gene.csv"
## [4] "L1_Haplotype_Os03g0845700_RAP2_gene.csv"
## [5] "L1_Haplotype_Os03g0845800_RAP2_gene.csv"
## [6] "L1_Haplotype_Os03g0848700_RAP2_gene.csv"
## [7] "L1_Haplotype_Os03g62400_gene_and_pheno.csv"
## [8] "L2_Haplotype_Os05g0420500_RAP2_gene.csv"
## [9] "L2_Haplotype_Os05g0420600_RAP2_gene.csv"
## [10] "L2_Haplotype_Os05g0420900_RAP2_gene.csv"
## [11] "L3_Haplotype_Os06g0346300_RAP2_gene.csv"
## [12] "L4_Haplotype_Os07g0623200_RAP2_gene.csv"
## [13] "L4_Haplotype_Os07g0623501_RAP2_gene.csv"
## [14] "L4_Haplotype_Os07g0623600_RAP2_gene.csv"
## [15] "L4_Haplotype_Os07g43040_gene.csv"
## [16] "L6_Haplotype_Os11g0216000_RAB2_gene.csv"
## [17] "Locus_1_final_file.csv"
## [18] "Locus_2_final_file.csv"
## [19] "Locus_3_final_file.csv"
## [20] "Locus_4_final_file.csv"
## [21] "Locus_6_final_file.csv"temp <- read.csv("L2_Haplotype_Os05g0420600_RAP2_gene.csv")
head(temp)haplotype2 <- temp[,c(1, 14)]
ultimate2 <- merge(pheno2, haplotype2, by=c("VCF_better"))
head(ultimate2)unique(ultimate2$haplotype)## [1] "AAAA" "ATAA" "TTAA"# let's see which haplotype is most popular among accessions:
ultimate2 %>% group_by(haplotype) %>%
tally()In this case - we have 6 original haplotypes - but only 1 of them is represented by 3 or more accessions
ultimate2$haplotype <- gsub("AAAA", "hap01", ultimate2$haplotype)
ultimate2$haplotype <- gsub("ATAA", "hap02", ultimate2$haplotype)
ultimate2$haplotype <- gsub("TTAA", "hap03", ultimate2$haplotype)
ultimate2$haplotype <- factor(ultimate2$haplotype, levels = c("hap01", "hap02", "hap03"))
colnames(ultimate2)## [1] "VCF_better" "HDRA.ID" "NSFTV.ID"
## [4] "IRGC.ID" "Subpop" "Accession.Name"
## [7] "VCF_code" "index.pots" "Variety"
## [10] "Shoot.area..cm2." "Hull.area..cm2." "Solidity"
## [13] "Perimeter..cm." "Nr.leaves" "Nr.tillers"
## [16] "Plant.height..cm." "Culm.height..cm." "Leaf.length..cm."
## [19] "DW..g." "Leaf.angle..º." "Tiller.angle..º."
## [22] "Erectness..º." "Droopiness..º." "SUM_rank_traits"
## [25] "SUM_norm_traits" "norm_SI_rank" "SI_rank"
## [28] "haplotype"Output <- TukeyHSD(aov(aov(Shoot.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Shoot.area..cm2., colour = haplotype))
my_box_plot <- my_box_plot + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot <- my_box_plot + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot <- my_box_plot + theme(legend.position = "none")
my_box_plot <- my_box_plot + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot <- my_box_plot + xlab("") + ylab(expression(paste("Shoot area (", cm^2, ")", sep = "")))
my_box_plot <- my_box_plot + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot <- my_box_plot + stat_pvalue_manual(test, label = "Tukey", y.position = 950)
my_box_plot
Output <- TukeyHSD(aov(aov(Hull.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot2 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Hull.area..cm2., colour = haplotype))
my_box_plot2 <- my_box_plot2 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot2 <- my_box_plot2 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot2 <- my_box_plot2 + theme(legend.position = "none")
my_box_plot2 <- my_box_plot2 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot2 <- my_box_plot2 + xlab("") + ylab(expression(paste("Hull area (", cm^2, ")", sep = "")))
my_box_plot2 <- my_box_plot2 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot2 <- my_box_plot2 + stat_pvalue_manual(test, label = "Tukey", y.position = 6000)
my_box_plot2
Output <- TukeyHSD(aov(aov(Solidity ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot3 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Solidity, colour = haplotype))
my_box_plot3 <- my_box_plot3 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot3 <- my_box_plot3 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot3 <- my_box_plot3 + theme(legend.position = "none")
my_box_plot3 <- my_box_plot3 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot3 <- my_box_plot3 + xlab("") + ylab("Solidity (a.u.)")
my_box_plot3 <- my_box_plot3 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot3 <- my_box_plot3 + stat_pvalue_manual(test, label = "Tukey", y.position = 0.21)
my_box_plot3
Output <- TukeyHSD(aov(aov(Perimeter..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot4 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Perimeter..cm., colour = haplotype))
my_box_plot4 <- my_box_plot4 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot4 <- my_box_plot4 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot4 <- my_box_plot4 + theme(legend.position = "none")
my_box_plot4 <- my_box_plot4 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot4 <- my_box_plot4 + xlab("") + ylab("Perimeter (cm)")
my_box_plot4 <- my_box_plot4 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot4 <- my_box_plot4 + stat_pvalue_manual(test, label = "Tukey", y.position = 2500)
my_box_plot4
Output <- TukeyHSD(aov(aov(Nr.leaves ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot5 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.leaves, colour = haplotype))
my_box_plot5 <- my_box_plot5 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot5 <- my_box_plot5 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot5 <- my_box_plot5 + theme(legend.position = "none")
my_box_plot5 <- my_box_plot5 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot5 <- my_box_plot5 + xlab("") + ylab("Leaf number")
my_box_plot5 <- my_box_plot5 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot5 <- my_box_plot5 + stat_pvalue_manual(test, label = "Tukey", y.position = 55)
my_box_plot5
Output <- TukeyHSD(aov(aov(Nr.tillers ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot6 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.tillers, colour = haplotype))
my_box_plot6 <- my_box_plot6 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot6 <- my_box_plot6 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot6 <- my_box_plot6 + theme(legend.position = "none")
my_box_plot6 <- my_box_plot6 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot6 <- my_box_plot6 + xlab("") + ylab("Tiller number")
my_box_plot6 <- my_box_plot6 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot6 <- my_box_plot6 + stat_pvalue_manual(test, label = "Tukey", y.position = 17)
my_box_plot6
Output <- TukeyHSD(aov(aov(Plant.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot7 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Plant.height..cm., colour = haplotype))
my_box_plot7 <- my_box_plot7 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot7 <- my_box_plot7 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot7 <- my_box_plot7 + theme(legend.position = "none")
my_box_plot7 <- my_box_plot7 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot7 <- my_box_plot7 + xlab("") + ylab("Plant height (cm)")
my_box_plot7 <- my_box_plot7 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot7 <- my_box_plot7 + stat_pvalue_manual(test, label = "Tukey", y.position = 95)
my_box_plot7
Output <- TukeyHSD(aov(aov(Culm.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot8 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Culm.height..cm., colour = haplotype))
my_box_plot8 <- my_box_plot8 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot8 <- my_box_plot8 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot8 <- my_box_plot8 + theme(legend.position = "none")
my_box_plot8 <- my_box_plot8 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot8 <- my_box_plot8 + xlab("") + ylab("Culm height (cm)")
my_box_plot8 <- my_box_plot8 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot8 <- my_box_plot8 + stat_pvalue_manual(test, label = "Tukey", y.position = 35)
my_box_plot8
Output <- TukeyHSD(aov(aov(Leaf.length..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot9 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.length..cm., colour = haplotype))
my_box_plot9 <- my_box_plot9 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot9 <- my_box_plot9 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot9 <- my_box_plot9 + theme(legend.position = "none")
my_box_plot9 <- my_box_plot9 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot9 <- my_box_plot9 + xlab("") + ylab("Leaf length (cm)")
my_box_plot9 <- my_box_plot9 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot9 <- my_box_plot9 + stat_pvalue_manual(test, label = "Tukey", y.position = 65)
my_box_plot9
Output <- TukeyHSD(aov(aov(DW..g. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot10 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = DW..g., colour = haplotype))
my_box_plot10 <- my_box_plot10 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot10 <- my_box_plot10 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot10 <- my_box_plot10 + theme(legend.position = "none")
my_box_plot10 <- my_box_plot10 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot10 <- my_box_plot10 + xlab("") + ylab("Dry weight (g)")
my_box_plot10 <- my_box_plot10 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot10 <- my_box_plot10 + stat_pvalue_manual(test, label = "Tukey", y.position = 4)
my_box_plot10
Output <- TukeyHSD(aov(aov(Leaf.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot11 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.angle..º., colour = haplotype))
my_box_plot11 <- my_box_plot11 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot11 <- my_box_plot11 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot11 <- my_box_plot11 + theme(legend.position = "none")
my_box_plot11 <- my_box_plot11 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot11 <- my_box_plot11 + xlab("") + ylab("Leaf angle (º)")
my_box_plot11 <- my_box_plot11 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot11 <- my_box_plot11 + stat_pvalue_manual(test, label = "Tukey", y.position = 65)
my_box_plot11
Output <- TukeyHSD(aov(aov(Tiller.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot12 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Tiller.angle..º., colour = haplotype))
my_box_plot12 <- my_box_plot12 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot12 <- my_box_plot12 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot12 <- my_box_plot12 + theme(legend.position = "none")
my_box_plot12 <- my_box_plot12 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot12 <- my_box_plot12 + xlab("") + ylab("Tiller angle (º)")
my_box_plot12 <- my_box_plot12 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot12 <- my_box_plot12 + stat_pvalue_manual(test, label = "Tukey", y.position = 37)
my_box_plot12
Output <- TukeyHSD(aov(aov(Erectness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot13 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Erectness..º., colour = haplotype))
my_box_plot13 <- my_box_plot13 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot13 <- my_box_plot13 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot13 <- my_box_plot13 + theme(legend.position = "none")
my_box_plot13 <- my_box_plot13 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot13 <- my_box_plot13 + xlab("") + ylab("Erectness (º)")
my_box_plot13 <- my_box_plot13 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot13 <- my_box_plot13 + stat_pvalue_manual(test, label = "Tukey", y.position = 165)
my_box_plot13
Output <- TukeyHSD(aov(aov(Droopiness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot14 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Droopiness..º., colour = haplotype))
my_box_plot14 <- my_box_plot14 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot14 <- my_box_plot14 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot14 <- my_box_plot14 + theme(legend.position = "none")
my_box_plot14 <- my_box_plot14 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot14 <- my_box_plot14 + xlab("") + ylab("Droopiness (º)")
my_box_plot14 <- my_box_plot14 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot14 <- my_box_plot14 + stat_pvalue_manual(test, label = "Tukey", y.position = 170)
my_box_plot14
pdf("Locus_02_Haplotypes_Os05g0420600_RAP2_NEW.pdf", height = 30, width = 12)
plot_grid(my_box_plot, my_box_plot2, my_box_plot3, my_box_plot4, my_box_plot5, my_box_plot6, my_box_plot7, my_box_plot8, my_box_plot9, my_box_plot10, my_box_plot11, my_box_plot12, my_box_plot13, my_box_plot14,
ncol=2,
align = "hv", labels=c("AUTO"),
label_size = 24)
dev.off()## quartz_off_screen
## 2Locus 2 Os05g0420900 RAP2
list.files(pattern=".csv")## [1] "L1_Haplotype_Os03g0841800_RAP2_gene_and_pheno.csv"
## [2] "L1_Haplotype_Os03g0843700_RAP2_gene.csv"
## [3] "L1_Haplotype_Os03g0845000_RAP2_gene.csv"
## [4] "L1_Haplotype_Os03g0845700_RAP2_gene.csv"
## [5] "L1_Haplotype_Os03g0845800_RAP2_gene.csv"
## [6] "L1_Haplotype_Os03g0848700_RAP2_gene.csv"
## [7] "L1_Haplotype_Os03g62400_gene_and_pheno.csv"
## [8] "L2_Haplotype_Os05g0420500_RAP2_gene.csv"
## [9] "L2_Haplotype_Os05g0420600_RAP2_gene.csv"
## [10] "L2_Haplotype_Os05g0420900_RAP2_gene.csv"
## [11] "L3_Haplotype_Os06g0346300_RAP2_gene.csv"
## [12] "L4_Haplotype_Os07g0623200_RAP2_gene.csv"
## [13] "L4_Haplotype_Os07g0623501_RAP2_gene.csv"
## [14] "L4_Haplotype_Os07g0623600_RAP2_gene.csv"
## [15] "L4_Haplotype_Os07g43040_gene.csv"
## [16] "L6_Haplotype_Os11g0216000_RAB2_gene.csv"
## [17] "Locus_1_final_file.csv"
## [18] "Locus_2_final_file.csv"
## [19] "Locus_3_final_file.csv"
## [20] "Locus_4_final_file.csv"
## [21] "Locus_6_final_file.csv"temp <- read.csv("L2_Haplotype_Os05g0420900_RAP2_gene.csv")
head(temp)haplotype2 <- temp[,c(1, 14)]
ultimate2 <- merge(pheno2, haplotype2, by=c("VCF_better"))
head(ultimate2)unique(ultimate2$haplotype)## [1] "AAAAAA" "AATAAA" "ATTAAA"# let's see which haplotype is most popular among accessions:
ultimate2 %>% group_by(haplotype) %>%
tally()In this case - we have 6 original haplotypes - but only 1 of them is represented by 3 or more accessions
ultimate2$haplotype <- gsub("AAAAAA", "hap01", ultimate2$haplotype)
ultimate2$haplotype <- gsub("AATAAA", "hap02", ultimate2$haplotype)
ultimate2$haplotype <- gsub("ATTAAA", "hap03", ultimate2$haplotype)
ultimate2$haplotype <- factor(ultimate2$haplotype, levels = c("hap01", "hap02", "hap03"))
colnames(ultimate2)## [1] "VCF_better" "HDRA.ID" "NSFTV.ID"
## [4] "IRGC.ID" "Subpop" "Accession.Name"
## [7] "VCF_code" "index.pots" "Variety"
## [10] "Shoot.area..cm2." "Hull.area..cm2." "Solidity"
## [13] "Perimeter..cm." "Nr.leaves" "Nr.tillers"
## [16] "Plant.height..cm." "Culm.height..cm." "Leaf.length..cm."
## [19] "DW..g." "Leaf.angle..º." "Tiller.angle..º."
## [22] "Erectness..º." "Droopiness..º." "SUM_rank_traits"
## [25] "SUM_norm_traits" "norm_SI_rank" "SI_rank"
## [28] "haplotype"Output <- TukeyHSD(aov(aov(Shoot.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Shoot.area..cm2., colour = haplotype))
my_box_plot <- my_box_plot + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot <- my_box_plot + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot <- my_box_plot + theme(legend.position = "none")
my_box_plot <- my_box_plot + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot <- my_box_plot + xlab("") + ylab(expression(paste("Shoot area (", cm^2, ")", sep = "")))
my_box_plot <- my_box_plot + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot <- my_box_plot + stat_pvalue_manual(test, label = "Tukey", y.position = 950)
my_box_plot
Output <- TukeyHSD(aov(aov(Hull.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot2 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Hull.area..cm2., colour = haplotype))
my_box_plot2 <- my_box_plot2 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot2 <- my_box_plot2 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot2 <- my_box_plot2 + theme(legend.position = "none")
my_box_plot2 <- my_box_plot2 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot2 <- my_box_plot2 + xlab("") + ylab(expression(paste("Hull area (", cm^2, ")", sep = "")))
my_box_plot2 <- my_box_plot2 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot2 <- my_box_plot2 + stat_pvalue_manual(test, label = "Tukey", y.position = 6000)
my_box_plot2
Output <- TukeyHSD(aov(aov(Solidity ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot3 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Solidity, colour = haplotype))
my_box_plot3 <- my_box_plot3 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot3 <- my_box_plot3 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot3 <- my_box_plot3 + theme(legend.position = "none")
my_box_plot3 <- my_box_plot3 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot3 <- my_box_plot3 + xlab("") + ylab("Solidity (a.u.)")
my_box_plot3 <- my_box_plot3 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot3 <- my_box_plot3 + stat_pvalue_manual(test, label = "Tukey", y.position = 0.21)
my_box_plot3
Output <- TukeyHSD(aov(aov(Perimeter..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot4 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Perimeter..cm., colour = haplotype))
my_box_plot4 <- my_box_plot4 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot4 <- my_box_plot4 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot4 <- my_box_plot4 + theme(legend.position = "none")
my_box_plot4 <- my_box_plot4 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot4 <- my_box_plot4 + xlab("") + ylab("Perimeter (cm)")
my_box_plot4 <- my_box_plot4 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot4 <- my_box_plot4 + stat_pvalue_manual(test, label = "Tukey", y.position = 2500)
my_box_plot4
Output <- TukeyHSD(aov(aov(Nr.leaves ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot5 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.leaves, colour = haplotype))
my_box_plot5 <- my_box_plot5 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot5 <- my_box_plot5 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot5 <- my_box_plot5 + theme(legend.position = "none")
my_box_plot5 <- my_box_plot5 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot5 <- my_box_plot5 + xlab("") + ylab("Leaf number")
my_box_plot5 <- my_box_plot5 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot5 <- my_box_plot5 + stat_pvalue_manual(test, label = "Tukey", y.position = 55)
my_box_plot5
Output <- TukeyHSD(aov(aov(Nr.tillers ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot6 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.tillers, colour = haplotype))
my_box_plot6 <- my_box_plot6 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot6 <- my_box_plot6 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot6 <- my_box_plot6 + theme(legend.position = "none")
my_box_plot6 <- my_box_plot6 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot6 <- my_box_plot6 + xlab("") + ylab("Tiller number")
my_box_plot6 <- my_box_plot6 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot6 <- my_box_plot6 + stat_pvalue_manual(test, label = "Tukey", y.position = 17)
my_box_plot6
Output <- TukeyHSD(aov(aov(Plant.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot7 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Plant.height..cm., colour = haplotype))
my_box_plot7 <- my_box_plot7 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot7 <- my_box_plot7 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot7 <- my_box_plot7 + theme(legend.position = "none")
my_box_plot7 <- my_box_plot7 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot7 <- my_box_plot7 + xlab("") + ylab("Plant height (cm)")
my_box_plot7 <- my_box_plot7 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot7 <- my_box_plot7 + stat_pvalue_manual(test, label = "Tukey", y.position = 95)
my_box_plot7
Output <- TukeyHSD(aov(aov(Culm.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot8 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Culm.height..cm., colour = haplotype))
my_box_plot8 <- my_box_plot8 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot8 <- my_box_plot8 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot8 <- my_box_plot8 + theme(legend.position = "none")
my_box_plot8 <- my_box_plot8 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot8 <- my_box_plot8 + xlab("") + ylab("Culm height (cm)")
my_box_plot8 <- my_box_plot8 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot8 <- my_box_plot8 + stat_pvalue_manual(test, label = "Tukey", y.position = 35)
my_box_plot8
Output <- TukeyHSD(aov(aov(Leaf.length..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot9 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.length..cm., colour = haplotype))
my_box_plot9 <- my_box_plot9 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot9 <- my_box_plot9 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot9 <- my_box_plot9 + theme(legend.position = "none")
my_box_plot9 <- my_box_plot9 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot9 <- my_box_plot9 + xlab("") + ylab("Leaf length (cm)")
my_box_plot9 <- my_box_plot9 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot9 <- my_box_plot9 + stat_pvalue_manual(test, label = "Tukey", y.position = 65)
my_box_plot9
Output <- TukeyHSD(aov(aov(DW..g. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot10 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = DW..g., colour = haplotype))
my_box_plot10 <- my_box_plot10 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot10 <- my_box_plot10 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot10 <- my_box_plot10 + theme(legend.position = "none")
my_box_plot10 <- my_box_plot10 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot10 <- my_box_plot10 + xlab("") + ylab("Dry weight (g)")
my_box_plot10 <- my_box_plot10 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot10 <- my_box_plot10 + stat_pvalue_manual(test, label = "Tukey", y.position = 4)
my_box_plot10
Output <- TukeyHSD(aov(aov(Leaf.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot11 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.angle..º., colour = haplotype))
my_box_plot11 <- my_box_plot11 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot11 <- my_box_plot11 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot11 <- my_box_plot11 + theme(legend.position = "none")
my_box_plot11 <- my_box_plot11 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot11 <- my_box_plot11 + xlab("") + ylab("Leaf angle (º)")
my_box_plot11 <- my_box_plot11 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot11 <- my_box_plot11 + stat_pvalue_manual(test, label = "Tukey", y.position = 65)
my_box_plot11
Output <- TukeyHSD(aov(aov(Tiller.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot12 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Tiller.angle..º., colour = haplotype))
my_box_plot12 <- my_box_plot12 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot12 <- my_box_plot12 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot12 <- my_box_plot12 + theme(legend.position = "none")
my_box_plot12 <- my_box_plot12 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot12 <- my_box_plot12 + xlab("") + ylab("Tiller angle (º)")
my_box_plot12 <- my_box_plot12 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot12 <- my_box_plot12 + stat_pvalue_manual(test, label = "Tukey", y.position = 37)
my_box_plot12
Output <- TukeyHSD(aov(aov(Erectness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot13 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Erectness..º., colour = haplotype))
my_box_plot13 <- my_box_plot13 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot13 <- my_box_plot13 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot13 <- my_box_plot13 + theme(legend.position = "none")
my_box_plot13 <- my_box_plot13 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot13 <- my_box_plot13 + xlab("") + ylab("Erectness (º)")
my_box_plot13 <- my_box_plot13 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot13 <- my_box_plot13 + stat_pvalue_manual(test, label = "Tukey", y.position = 165)
my_box_plot13
Output <- TukeyHSD(aov(aov(Droopiness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot14 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Droopiness..º., colour = haplotype))
my_box_plot14 <- my_box_plot14 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot14 <- my_box_plot14 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot14 <- my_box_plot14 + theme(legend.position = "none")
my_box_plot14 <- my_box_plot14 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3"))
my_box_plot14 <- my_box_plot14 + xlab("") + ylab("Droopiness (º)")
my_box_plot14 <- my_box_plot14 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot14 <- my_box_plot14 + stat_pvalue_manual(test, label = "Tukey", y.position = 170)
my_box_plot14
pdf("Locus_02_Haplotypes_Os05g0420900_RAP2_NEW.pdf", height = 30, width = 12)
plot_grid(my_box_plot, my_box_plot2, my_box_plot3, my_box_plot4, my_box_plot5, my_box_plot6, my_box_plot7, my_box_plot8, my_box_plot9, my_box_plot10, my_box_plot11, my_box_plot12, my_box_plot13, my_box_plot14,
ncol=2,
align = "hv", labels=c("AUTO"),
label_size = 24)
dev.off()## quartz_off_screen
## 2Locus 4 Os07g0623200
list.files(pattern=".csv")## [1] "L1_Haplotype_Os03g0841800_RAP2_gene_and_pheno.csv"
## [2] "L1_Haplotype_Os03g0843700_RAP2_gene.csv"
## [3] "L1_Haplotype_Os03g0845000_RAP2_gene.csv"
## [4] "L1_Haplotype_Os03g0845700_RAP2_gene.csv"
## [5] "L1_Haplotype_Os03g0845800_RAP2_gene.csv"
## [6] "L1_Haplotype_Os03g0848700_RAP2_gene.csv"
## [7] "L1_Haplotype_Os03g62400_gene_and_pheno.csv"
## [8] "L2_Haplotype_Os05g0420500_RAP2_gene.csv"
## [9] "L2_Haplotype_Os05g0420600_RAP2_gene.csv"
## [10] "L2_Haplotype_Os05g0420900_RAP2_gene.csv"
## [11] "L3_Haplotype_Os06g0346300_RAP2_gene.csv"
## [12] "L4_Haplotype_Os07g0623200_RAP2_gene.csv"
## [13] "L4_Haplotype_Os07g0623501_RAP2_gene.csv"
## [14] "L4_Haplotype_Os07g0623600_RAP2_gene.csv"
## [15] "L4_Haplotype_Os07g43040_gene.csv"
## [16] "L6_Haplotype_Os11g0216000_RAB2_gene.csv"
## [17] "Locus_1_final_file.csv"
## [18] "Locus_2_final_file.csv"
## [19] "Locus_3_final_file.csv"
## [20] "Locus_4_final_file.csv"
## [21] "Locus_6_final_file.csv"temp <- read.csv("L4_Haplotype_Os07g0623200_RAP2_gene.csv")
head(temp)haplotype2 <- temp[,c(1, 14)]
ultimate2 <- merge(pheno2, haplotype2, by=c("VCF_better"))
head(ultimate2)unique(ultimate2$haplotype)## [1] "AAAA" "ATAA" "ATAT" "AATA"# let's see which haplotype is most popular among accessions:
ultimate2 %>% group_by(haplotype) %>%
tally()In this case - we have 6 original haplotypes - but only 1 of them is represented by 3 or more accessions
ultimate2$haplotype <- gsub("AAAA", "hap01", ultimate2$haplotype)
ultimate2$haplotype <- gsub("ATAA", "hap02", ultimate2$haplotype)
ultimate2$haplotype <- gsub("ATAT", "hap03", ultimate2$haplotype)
ultimate2$haplotype <- gsub("AATA", "hap04", ultimate2$haplotype)
ultimate2$haplotype <- factor(ultimate2$haplotype, levels = c("hap01", "hap02", "hap03", "hap04"))
colnames(ultimate2)## [1] "VCF_better" "HDRA.ID" "NSFTV.ID"
## [4] "IRGC.ID" "Subpop" "Accession.Name"
## [7] "VCF_code" "index.pots" "Variety"
## [10] "Shoot.area..cm2." "Hull.area..cm2." "Solidity"
## [13] "Perimeter..cm." "Nr.leaves" "Nr.tillers"
## [16] "Plant.height..cm." "Culm.height..cm." "Leaf.length..cm."
## [19] "DW..g." "Leaf.angle..º." "Tiller.angle..º."
## [22] "Erectness..º." "Droopiness..º." "SUM_rank_traits"
## [25] "SUM_norm_traits" "norm_SI_rank" "SI_rank"
## [28] "haplotype"Output <- TukeyHSD(aov(aov(Shoot.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Shoot.area..cm2., colour = haplotype))
my_box_plot <- my_box_plot + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot <- my_box_plot + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot <- my_box_plot + theme(legend.position = "none")
my_box_plot <- my_box_plot + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot <- my_box_plot + xlab("") + ylab(expression(paste("Shoot area (", cm^2, ")", sep = "")))
my_box_plot <- my_box_plot + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot <- my_box_plot + stat_pvalue_manual(test, label = "Tukey", y.position = 950)
my_box_plot
Output <- TukeyHSD(aov(aov(Hull.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot2 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Hull.area..cm2., colour = haplotype))
my_box_plot2 <- my_box_plot2 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot2 <- my_box_plot2 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot2 <- my_box_plot2 + theme(legend.position = "none")
my_box_plot2 <- my_box_plot2 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot2 <- my_box_plot2 + xlab("") + ylab(expression(paste("Hull area (", cm^2, ")", sep = "")))
my_box_plot2 <- my_box_plot2 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot2 <- my_box_plot2 + stat_pvalue_manual(test, label = "Tukey", y.position = 6000)
my_box_plot2
Output <- TukeyHSD(aov(aov(Solidity ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot3 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Solidity, colour = haplotype))
my_box_plot3 <- my_box_plot3 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot3 <- my_box_plot3 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot3 <- my_box_plot3 + theme(legend.position = "none")
my_box_plot3 <- my_box_plot3 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot3 <- my_box_plot3 + xlab("") + ylab("Solidity (a.u.)")
my_box_plot3 <- my_box_plot3 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot3 <- my_box_plot3 + stat_pvalue_manual(test, label = "Tukey", y.position = 0.21)
my_box_plot3
Output <- TukeyHSD(aov(aov(Perimeter..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot4 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Perimeter..cm., colour = haplotype))
my_box_plot4 <- my_box_plot4 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot4 <- my_box_plot4 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot4 <- my_box_plot4 + theme(legend.position = "none")
my_box_plot4 <- my_box_plot4 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot4 <- my_box_plot4 + xlab("") + ylab("Perimeter (cm)")
my_box_plot4 <- my_box_plot4 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot4 <- my_box_plot4 + stat_pvalue_manual(test, label = "Tukey", y.position = 2500)
my_box_plot4
Output <- TukeyHSD(aov(aov(Nr.leaves ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot5 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.leaves, colour = haplotype))
my_box_plot5 <- my_box_plot5 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot5 <- my_box_plot5 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot5 <- my_box_plot5 + theme(legend.position = "none")
my_box_plot5 <- my_box_plot5 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot5 <- my_box_plot5 + xlab("") + ylab("Leaf number")
my_box_plot5 <- my_box_plot5 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot5 <- my_box_plot5 + stat_pvalue_manual(test, label = "Tukey", y.position = 55)
my_box_plot5
Output <- TukeyHSD(aov(aov(Nr.tillers ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot6 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.tillers, colour = haplotype))
my_box_plot6 <- my_box_plot6 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot6 <- my_box_plot6 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot6 <- my_box_plot6 + theme(legend.position = "none")
my_box_plot6 <- my_box_plot6 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot6 <- my_box_plot6 + xlab("") + ylab("Tiller number")
my_box_plot6 <- my_box_plot6 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot6 <- my_box_plot6 + stat_pvalue_manual(test, label = "Tukey", y.position = 17)
my_box_plot6
Output <- TukeyHSD(aov(aov(Plant.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot7 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Plant.height..cm., colour = haplotype))
my_box_plot7 <- my_box_plot7 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot7 <- my_box_plot7 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot7 <- my_box_plot7 + theme(legend.position = "none")
my_box_plot7 <- my_box_plot7 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot7 <- my_box_plot7 + xlab("") + ylab("Plant height (cm)")
my_box_plot7 <- my_box_plot7 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot7 <- my_box_plot7 + stat_pvalue_manual(test, label = "Tukey", y.position = 95)
my_box_plot7
Output <- TukeyHSD(aov(aov(Culm.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot8 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Culm.height..cm., colour = haplotype))
my_box_plot8 <- my_box_plot8 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot8 <- my_box_plot8 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot8 <- my_box_plot8 + theme(legend.position = "none")
my_box_plot8 <- my_box_plot8 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot8 <- my_box_plot8 + xlab("") + ylab("Culm height (cm)")
my_box_plot8 <- my_box_plot8 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot8 <- my_box_plot8 + stat_pvalue_manual(test, label = "Tukey", y.position = 35)
my_box_plot8
Output <- TukeyHSD(aov(aov(Leaf.length..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot9 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.length..cm., colour = haplotype))
my_box_plot9 <- my_box_plot9 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot9 <- my_box_plot9 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot9 <- my_box_plot9 + theme(legend.position = "none")
my_box_plot9 <- my_box_plot9 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot9 <- my_box_plot9 + xlab("") + ylab("Leaf length (cm)")
my_box_plot9 <- my_box_plot9 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot9 <- my_box_plot9 + stat_pvalue_manual(test, label = "Tukey", y.position = 65)
my_box_plot9
Output <- TukeyHSD(aov(aov(DW..g. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot10 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = DW..g., colour = haplotype))
my_box_plot10 <- my_box_plot10 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot10 <- my_box_plot10 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot10 <- my_box_plot10 + theme(legend.position = "none")
my_box_plot10 <- my_box_plot10 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot10 <- my_box_plot10 + xlab("") + ylab("Dry weight (g)")
my_box_plot10 <- my_box_plot10 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot10 <- my_box_plot10 + stat_pvalue_manual(test, label = "Tukey", y.position = 4)
my_box_plot10
Output <- TukeyHSD(aov(aov(Leaf.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot11 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.angle..º., colour = haplotype))
my_box_plot11 <- my_box_plot11 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot11 <- my_box_plot11 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot11 <- my_box_plot11 + theme(legend.position = "none")
my_box_plot11 <- my_box_plot11 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot11 <- my_box_plot11 + xlab("") + ylab("Leaf angle (º)")
my_box_plot11 <- my_box_plot11 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot11 <- my_box_plot11 + stat_pvalue_manual(test, label = "Tukey", y.position = 65)
my_box_plot11
Output <- TukeyHSD(aov(aov(Tiller.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot12 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Tiller.angle..º., colour = haplotype))
my_box_plot12 <- my_box_plot12 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot12 <- my_box_plot12 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot12 <- my_box_plot12 + theme(legend.position = "none")
my_box_plot12 <- my_box_plot12 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot12 <- my_box_plot12 + xlab("") + ylab("Tiller angle (º)")
my_box_plot12 <- my_box_plot12 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot12 <- my_box_plot12 + stat_pvalue_manual(test, label = "Tukey", y.position = 37)
my_box_plot12
Output <- TukeyHSD(aov(aov(Erectness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot13 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Erectness..º., colour = haplotype))
my_box_plot13 <- my_box_plot13 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot13 <- my_box_plot13 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot13 <- my_box_plot13 + theme(legend.position = "none")
my_box_plot13 <- my_box_plot13 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot13 <- my_box_plot13 + xlab("") + ylab("Erectness (º)")
my_box_plot13 <- my_box_plot13 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot13 <- my_box_plot13 + stat_pvalue_manual(test, label = "Tukey", y.position = 165)
my_box_plot13
Output <- TukeyHSD(aov(aov(Droopiness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
stat.test<- multcompLetters(P4)
test <- as.data.frame(stat.test$Letters)
test$group1 <- rownames(test)
test$group2 <- rownames(test)
colnames(test)[1] <- "Tukey"
my_box_plot14 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Droopiness..º., colour = haplotype))
my_box_plot14 <- my_box_plot14 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot14 <- my_box_plot14 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot14 <- my_box_plot14 + theme(legend.position = "none")
my_box_plot14 <- my_box_plot14 + scale_colour_manual(values = c("steelblue", "firebrick3", "firebrick3", "firebrick3"))
my_box_plot14 <- my_box_plot14 + xlab("") + ylab("Droopiness (º)")
my_box_plot14 <- my_box_plot14 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot14 <- my_box_plot14 + stat_pvalue_manual(test, label = "Tukey", y.position = 170)
my_box_plot14
pdf("Locus_04_Haplotypes_Os07g0623200_RAP2_NEW.pdf", height = 30, width = 12)
plot_grid(my_box_plot, my_box_plot2, my_box_plot3, my_box_plot4, my_box_plot5, my_box_plot6, my_box_plot7, my_box_plot8, my_box_plot9, my_box_plot10, my_box_plot11, my_box_plot12, my_box_plot13, my_box_plot14,
ncol=2,
align = "hv", labels=c("AUTO"),
label_size = 24)
dev.off()## quartz_off_screen
## 2Locus 6 Os11g0216000
list.files(pattern=".csv")## [1] "L1_Haplotype_Os03g0841800_RAP2_gene_and_pheno.csv"
## [2] "L1_Haplotype_Os03g0843700_RAP2_gene.csv"
## [3] "L1_Haplotype_Os03g0845000_RAP2_gene.csv"
## [4] "L1_Haplotype_Os03g0845700_RAP2_gene.csv"
## [5] "L1_Haplotype_Os03g0845800_RAP2_gene.csv"
## [6] "L1_Haplotype_Os03g0848700_RAP2_gene.csv"
## [7] "L1_Haplotype_Os03g62400_gene_and_pheno.csv"
## [8] "L2_Haplotype_Os05g0420500_RAP2_gene.csv"
## [9] "L2_Haplotype_Os05g0420600_RAP2_gene.csv"
## [10] "L2_Haplotype_Os05g0420900_RAP2_gene.csv"
## [11] "L3_Haplotype_Os06g0346300_RAP2_gene.csv"
## [12] "L4_Haplotype_Os07g0623200_RAP2_gene.csv"
## [13] "L4_Haplotype_Os07g0623501_RAP2_gene.csv"
## [14] "L4_Haplotype_Os07g0623600_RAP2_gene.csv"
## [15] "L4_Haplotype_Os07g43040_gene.csv"
## [16] "L6_Haplotype_Os11g0216000_RAB2_gene.csv"
## [17] "Locus_1_final_file.csv"
## [18] "Locus_2_final_file.csv"
## [19] "Locus_3_final_file.csv"
## [20] "Locus_4_final_file.csv"
## [21] "Locus_6_final_file.csv"temp <- read.csv("L6_Haplotype_Os11g0216000_RAB2_gene.csv")
head(temp)haplotype2 <- temp[,c(1, 14)]
ultimate2 <- merge(pheno2, haplotype2, by=c("VCF_better"))
head(ultimate2)unique(ultimate2$haplotype)## [1] "AAAAAAAAA" "AAAATAAAA"# let's see which haplotype is most popular among accessions:
ultimate2 %>% group_by(haplotype) %>%
tally()ultimate2$haplotype <- gsub("AAAAAAAAA", "hap01", ultimate2$haplotype)
ultimate2$haplotype <- gsub("AAAATAAAA", "hap02", ultimate2$haplotype)
ultimate2$haplotype <- factor(ultimate2$haplotype, levels = c("hap01", "hap02"))
colnames(ultimate2)## [1] "VCF_better" "HDRA.ID" "NSFTV.ID"
## [4] "IRGC.ID" "Subpop" "Accession.Name"
## [7] "VCF_code" "index.pots" "Variety"
## [10] "Shoot.area..cm2." "Hull.area..cm2." "Solidity"
## [13] "Perimeter..cm." "Nr.leaves" "Nr.tillers"
## [16] "Plant.height..cm." "Culm.height..cm." "Leaf.length..cm."
## [19] "DW..g." "Leaf.angle..º." "Tiller.angle..º."
## [22] "Erectness..º." "Droopiness..º." "SUM_rank_traits"
## [25] "SUM_norm_traits" "norm_SI_rank" "SI_rank"
## [28] "haplotype"OK - now let’s graph them:
Output <- TukeyHSD(aov(aov(Shoot.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 3.952704e-09my_box_plot <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Shoot.area..cm2., colour = haplotype))
my_box_plot <- my_box_plot + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot <- my_box_plot + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot <- my_box_plot + theme(legend.position = "none")
my_box_plot <- my_box_plot + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot <- my_box_plot + xlab("") + ylab(expression(paste("Shoot area (", cm^2, ")", sep = "")))
my_box_plot <- my_box_plot + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot <- my_box_plot + stat_pvalue_manual(test2, label = "Tukey", y.position = 950)
my_box_plot
Output <- TukeyHSD(aov(aov(Hull.area..cm2. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 7.073674e-08my_box_plot2 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Hull.area..cm2., colour = haplotype))
my_box_plot2 <- my_box_plot2 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot2 <- my_box_plot2 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot2 <- my_box_plot2 + theme(legend.position = "none")
my_box_plot2 <- my_box_plot2 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot2 <- my_box_plot2 + xlab("") + ylab(expression(paste("Hull area (", cm^2, ")", sep = "")))
my_box_plot2 <- my_box_plot2 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot2 <- my_box_plot2 + stat_pvalue_manual(test2, label = "Tukey", y.position = 6000)
my_box_plot2
Output <- TukeyHSD(aov(aov(Solidity ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0.0452482my_box_plot3 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Solidity, colour = haplotype))
my_box_plot3 <- my_box_plot3 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot3 <- my_box_plot3 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot3 <- my_box_plot3 + theme(legend.position = "none")
my_box_plot3 <- my_box_plot3 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot3 <- my_box_plot3 + xlab("") + ylab("Solidity (a.u.)")
my_box_plot3 <- my_box_plot3 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot3 <- my_box_plot3 + stat_pvalue_manual(test2, label = "Tukey", y.position = 0.21)
my_box_plot3
Output <- TukeyHSD(aov(aov(Perimeter..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 1.671474e-11my_box_plot4 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Perimeter..cm., colour = haplotype))
my_box_plot4 <- my_box_plot4 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot4 <- my_box_plot4 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot4 <- my_box_plot4 + theme(legend.position = "none")
my_box_plot4 <- my_box_plot4 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot4 <- my_box_plot4 + xlab("") + ylab("Perimeter (cm)")
my_box_plot4 <- my_box_plot4 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot4 <- my_box_plot4 + stat_pvalue_manual(test2, label = "Tukey", y.position = 2500)
my_box_plot4
Output <- TukeyHSD(aov(aov(Nr.leaves ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0my_box_plot5 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.leaves, colour = haplotype))
my_box_plot5 <- my_box_plot5 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot5 <- my_box_plot5 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot5 <- my_box_plot5 + theme(legend.position = "none")
my_box_plot5 <- my_box_plot5 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot5 <- my_box_plot5 + xlab("") + ylab("Leaf number")
my_box_plot5 <- my_box_plot5 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot5 <- my_box_plot5 + stat_pvalue_manual(test2, label = "Tukey", y.position = 55)
my_box_plot5
Output <- TukeyHSD(aov(aov(Nr.tillers ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0my_box_plot6 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Nr.tillers, colour = haplotype))
my_box_plot6 <- my_box_plot6 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot6 <- my_box_plot6 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot6 <- my_box_plot6 + theme(legend.position = "none")
my_box_plot6 <- my_box_plot6 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot6 <- my_box_plot6 + xlab("") + ylab("Tiller number")
my_box_plot6 <- my_box_plot6 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot6 <- my_box_plot6 + stat_pvalue_manual(test2, label = "Tukey", y.position = 17)
my_box_plot6
Output <- TukeyHSD(aov(aov(Plant.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0.5464665my_box_plot7 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Plant.height..cm., colour = haplotype))
my_box_plot7 <- my_box_plot7 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot7 <- my_box_plot7 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot7 <- my_box_plot7 + theme(legend.position = "none")
my_box_plot7 <- my_box_plot7 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot7 <- my_box_plot7 + xlab("") + ylab("Plant height (cm)")
my_box_plot7 <- my_box_plot7 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot7 <- my_box_plot7 + stat_pvalue_manual(test3, label = "Tukey", y.position = 95)
my_box_plot7
Output <- TukeyHSD(aov(aov(Culm.height..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0.01020817my_box_plot8 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Culm.height..cm., colour = haplotype))
my_box_plot8 <- my_box_plot8 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot8 <- my_box_plot8 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot8 <- my_box_plot8 + theme(legend.position = "none")
my_box_plot8 <- my_box_plot8 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot8 <- my_box_plot8 + xlab("") + ylab("Culm height (cm)")
my_box_plot8 <- my_box_plot8 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot8 <- my_box_plot8 + stat_pvalue_manual(test2, label = "Tukey", y.position = 35)
my_box_plot8
Output <- TukeyHSD(aov(aov(Leaf.length..cm. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0.9102221my_box_plot9 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.length..cm., colour = haplotype))
my_box_plot9 <- my_box_plot9 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot9 <- my_box_plot9 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot9 <- my_box_plot9 + theme(legend.position = "none")
my_box_plot9 <- my_box_plot9 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot9 <- my_box_plot9 + xlab("") + ylab("Leaf length (cm)")
my_box_plot9 <- my_box_plot9 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot9 <- my_box_plot9 + stat_pvalue_manual(test3, label = "Tukey", y.position = 65)
my_box_plot9
Output <- TukeyHSD(aov(aov(DW..g. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 1.336687e-08my_box_plot10 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = DW..g., colour = haplotype))
my_box_plot10 <- my_box_plot10 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot10 <- my_box_plot10 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot10 <- my_box_plot10 + theme(legend.position = "none")
my_box_plot10 <- my_box_plot10 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot10 <- my_box_plot10 + xlab("") + ylab("Dry weight (g)")
my_box_plot10 <- my_box_plot10 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot10 <- my_box_plot10 + stat_pvalue_manual(test2, label = "Tukey", y.position = 4)
my_box_plot10
Output <- TukeyHSD(aov(aov(Leaf.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0.6813148my_box_plot11 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Leaf.angle..º., colour = haplotype))
my_box_plot11 <- my_box_plot11 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot11 <- my_box_plot11 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot11 <- my_box_plot11 + theme(legend.position = "none")
my_box_plot11 <- my_box_plot11 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot11 <- my_box_plot11 + xlab("") + ylab("Leaf angle (º)")
my_box_plot11 <- my_box_plot11 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot11 <- my_box_plot11 + stat_pvalue_manual(test3, label = "Tukey", y.position = 65)
my_box_plot11
Output <- TukeyHSD(aov(aov(Tiller.angle..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 2.522885e-05my_box_plot12 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Tiller.angle..º., colour = haplotype))
my_box_plot12 <- my_box_plot12 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot12 <- my_box_plot12 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot12 <- my_box_plot12 + theme(legend.position = "none")
my_box_plot12 <- my_box_plot12 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot12 <- my_box_plot12 + xlab("") + ylab("Tiller angle (º)")
my_box_plot12 <- my_box_plot12 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot12 <- my_box_plot12 + stat_pvalue_manual(test2, label = "Tukey", y.position = 37)
my_box_plot12
Output <- TukeyHSD(aov(aov(Erectness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0.2157439my_box_plot13 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Erectness..º., colour = haplotype))
my_box_plot13 <- my_box_plot13 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot13 <- my_box_plot13 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot13 <- my_box_plot13 + theme(legend.position = "none")
my_box_plot13 <- my_box_plot13 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot13 <- my_box_plot13 + xlab("") + ylab("Erectness (º)")
my_box_plot13 <- my_box_plot13 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot13 <- my_box_plot13 + stat_pvalue_manual(test3, label = "Tukey", y.position = 165)
my_box_plot13
Output <- TukeyHSD(aov(aov(Droopiness..º. ~ haplotype, data = ultimate2)))
P4 = Output$haplotype[,'p adj']
P4## [1] 0.2157439my_box_plot14 <- ggplot(data = ultimate2, mapping = aes(x = haplotype, y = Droopiness..º., colour = haplotype))
my_box_plot14 <- my_box_plot14 + geom_beeswarm(alpha=0.6, priority = "density")
my_box_plot14 <- my_box_plot14 + stat_summary(fun.y=mean, geom="point", shape=95, size=6, color="black", fill="black")## Warning: `fun.y` is deprecated. Use `fun` instead.my_box_plot14 <- my_box_plot14 + theme(legend.position = "none")
my_box_plot14 <- my_box_plot14 + scale_colour_manual(values = c("steelblue", "firebrick3"))
my_box_plot14 <- my_box_plot14 + xlab("") + ylab("Droopiness (º)")
my_box_plot14 <- my_box_plot14 + theme(axis.text.x = element_text(angle=90, hjust=0.9, vjust=0.5))
my_box_plot14 <- my_box_plot14 + stat_pvalue_manual(test3, label = "Tukey", y.position = 170)
my_box_plot14
pdf("Locus_06_Haplotypes_Os11g216000_RAP2_NEW.pdf", height = 30, width = 12)
plot_grid(my_box_plot, my_box_plot2, my_box_plot3, my_box_plot4, my_box_plot5, my_box_plot6,
my_box_plot7, my_box_plot8, my_box_plot9, my_box_plot10, my_box_plot11, my_box_plot12,
my_box_plot13, my_box_plot14,
ncol=2,
align = "hv", labels=c("AUTO"),
label_size = 24)
dev.off()## quartz_off_screen
## 2