Xianqin_Fig4A
library(plyr)## Warning: package 'plyr' was built under R version 4.1.2library(dplyr)## Warning: package 'dplyr' was built under R version 4.1.2##
## Attaching package: 'dplyr'## The following objects are masked from 'package:plyr':
##
## arrange, count, desc, failwith, id, mutate, rename, summarise,
## summarize## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionlibrary(ggplot2)## Warning: package 'ggplot2' was built under R version 4.1.2library(car)## Loading required package: carData##
## Attaching package: 'car'## The following object is masked from 'package:dplyr':
##
## recodeR script for Figure 4A
setwd("~/Desktop")
tab <- read.csv("~/Desktop/Fig4A1.csv")
str(tab)## 'data.frame': 240 obs. of 4 variables:
## $ Concentration: num 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 ...
## $ Compound : int 1 1 1 1 1 1 1 1 1 1 ...
## $ Group : int 0 0 0 0 0 1 1 1 1 1 ...
## $ Number : int 0 1 2 0 2 0 0 2 2 1 ...tab$Compound <- as.factor(tab$Compound)
tab$Group <-as.factor(tab$Group)
tab$Concentration <- as.factor(tab$Concentration)
hist(tab$Number)
tab$Compound <- revalue(tab$Compound,
c( "1"="Isocarophyllene",
"2"="Menthone",
"3"="Anethole",
"4"="Cineole",
"5"="Carvone",
"6"="Decadiene"))
tab$Group <- revalue(tab$Group, c("0"="Blank", "1"="Pure compound"))Create figure
names(tab)## [1] "Concentration" "Compound" "Group" "Number"tabm<-ddply(tab, c("Compound", "Concentration", "Group"), summarise,
mean = mean(Number), sd = sd(Number),
sem = sd(Number)/sqrt(length(Number)))
value_max = tabm %>%
dplyr::group_by(Concentration) %>%
dplyr::summarize(max_value = max(mean), sd = sd(mean))
tabm$Group## [1] Blank Pure compound Blank Pure compound Blank
## [6] Pure compound Blank Pure compound Blank Pure compound
## [11] Blank Pure compound Blank Pure compound Blank
## [16] Pure compound Blank Pure compound Blank Pure compound
## [21] Blank Pure compound Blank Pure compound Blank
## [26] Pure compound Blank Pure compound Blank Pure compound
## [31] Blank Pure compound Blank Pure compound Blank
## [36] Pure compound Blank Pure compound Blank Pure compound
## [41] Blank Pure compound Blank Pure compound Blank
## [46] Pure compound Blank Pure compound
## Levels: Blank Pure compoundtabm <- tabm %>%
mutate(mean = ifelse(Group == "Pure compound",
mean, -1*mean))
##
fig4a<-ggplot(tabm, aes(x=Concentration, y=mean, fill=Group)) +
geom_bar( stat="identity") +
geom_errorbar(aes(ymin=mean-sem, ymax=mean+sem),
width=.2, color = "grey20")+
coord_flip() +
theme_bw()+
scale_y_continuous(labels = abs)+
facet_grid(rows = vars(Compound)) + theme(legend.position = "top")+
xlab("Concentration (mg/l)") +
ylab("Number of nematodes") +
scale_fill_brewer(palette="Blues")+
theme(axis.text = element_text(size = 10))+
theme(axis.title = element_text(size = 12))
fig4a + facet_wrap(~ Compound, ncol=2)
names(tab)## [1] "Concentration" "Compound" "Group" "Number"hist(tab$Number)
fit<-glm(Number~Concentration*Compound*Group, data = tab, family = "quasipoisson")
summary(fit)##
## Call:
## glm(formula = Number ~ Concentration * Compound * Group, family = "quasipoisson",
## data = tab)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.3664 -1.0955 -0.3257 0.6734 2.2038
##
## Coefficients:
## Estimate Std. Error
## (Intercept) -9.287e-15 5.108e-01
## Concentration0.01 7.885e-01 6.161e-01
## Concentration0.1 1.030e+00 5.951e-01
## Concentration1 1.386e+00 5.711e-01
## CompoundMenthone 9.555e-01 6.011e-01
## CompoundAnethole 3.365e-01 6.688e-01
## CompoundCineole 1.224e+00 5.811e-01
## CompoundCarvone 3.365e-01 6.688e-01
## CompoundDecadiene 4.700e-01 6.512e-01
## GroupPure compound 2.600e-15 7.224e-01
## Concentration0.01:CompoundMenthone -7.143e-01 7.570e-01
## Concentration0.1:CompoundMenthone -1.030e+00 7.449e-01
## Concentration1:CompoundMenthone -1.061e+00 7.064e-01
## Concentration0.01:CompoundAnethole -2.495e-01 8.214e-01
## Concentration0.1:CompoundAnethole -4.906e-01 8.057e-01
## Concentration1:CompoundAnethole -2.412e-01 7.562e-01
## Concentration0.01:CompoundCineole -4.436e-01 7.146e-01
## Concentration0.1:CompoundCineole -1.224e+00 7.239e-01
## Concentration1:CompoundCineole -1.329e+00 6.895e-01
## Concentration0.01:CompoundCarvone -4.318e-01 8.345e-01
## Concentration0.1:CompoundCarvone -8.516e-02 7.829e-01
## Concentration1:CompoundCarvone -6.931e-01 7.783e-01
## Concentration0.01:CompoundDecadiene -2.288e-01 7.974e-01
## Concentration0.1:CompoundDecadiene -1.133e-01 7.632e-01
## Concentration1:CompoundDecadiene -5.754e-01 7.495e-01
## Concentration0.01:GroupPure compound -1.299e+00 1.037e+00
## Concentration0.1:GroupPure compound -8.473e-01 9.124e-01
## Concentration1:GroupPure compound -1.897e+00 1.011e+00
## CompoundMenthone:GroupPure compound -2.565e+00 1.388e+00
## CompoundAnethole:GroupPure compound -8.473e-01 1.069e+00
## CompoundCineole:GroupPure compound -1.735e+00 1.017e+00
## CompoundCarvone:GroupPure compound -8.473e-01 1.069e+00
## CompoundDecadiene:GroupPure compound -1.677e+01 1.074e+03
## Concentration0.01:CompoundMenthone:GroupPure compound 2.324e+00 1.734e+00
## Concentration0.1:CompoundMenthone:GroupPure compound 1.946e+00 1.665e+00
## Concentration1:CompoundMenthone:GroupPure compound 2.265e+00 1.775e+00
## Concentration0.01:CompoundAnethole:GroupPure compound 3.548e-01 1.568e+00
## Concentration0.1:CompoundAnethole:GroupPure compound 8.191e-01 1.350e+00
## Concentration1:CompoundAnethole:GroupPure compound -3.466e-01 1.734e+00
## Concentration0.01:CompoundCineole:GroupPure compound 9.544e-01 1.441e+00
## Concentration0.1:CompoundCineole:GroupPure compound 1.041e+00 1.368e+00
## Concentration1:CompoundCineole:GroupPure compound 2.128e+00 1.390e+00
## Concentration0.01:CompoundCarvone:GroupPure compound 9.426e-01 1.504e+00
## Concentration0.1:CompoundCarvone:GroupPure compound 1.905e-01 1.361e+00
## Concentration1:CompoundCarvone:GroupPure compound 7.985e-01 1.546e+00
## Concentration0.01:CompoundDecadiene:GroupPure compound 1.682e+01 1.074e+03
## Concentration0.1:CompoundDecadiene:GroupPure compound 1.572e+01 1.074e+03
## Concentration1:CompoundDecadiene:GroupPure compound 1.578e+01 1.074e+03
## t value Pr(>|t|)
## (Intercept) 0.000 1.0000
## Concentration0.01 1.280 0.2021
## Concentration0.1 1.730 0.0852 .
## Concentration1 2.427 0.0161 *
## CompoundMenthone 1.590 0.1135
## CompoundAnethole 0.503 0.6155
## CompoundCineole 2.106 0.0365 *
## CompoundCarvone 0.503 0.6155
## CompoundDecadiene 0.722 0.4713
## GroupPure compound 0.000 1.0000
## Concentration0.01:CompoundMenthone -0.944 0.3465
## Concentration0.1:CompoundMenthone -1.382 0.1685
## Concentration1:CompoundMenthone -1.502 0.1348
## Concentration0.01:CompoundAnethole -0.304 0.7617
## Concentration0.1:CompoundAnethole -0.609 0.5433
## Concentration1:CompoundAnethole -0.319 0.7501
## Concentration0.01:CompoundCineole -0.621 0.5355
## Concentration0.1:CompoundCineole -1.691 0.0926 .
## Concentration1:CompoundCineole -1.928 0.0554 .
## Concentration0.01:CompoundCarvone -0.517 0.6055
## Concentration0.1:CompoundCarvone -0.109 0.9135
## Concentration1:CompoundCarvone -0.891 0.3742
## Concentration0.01:CompoundDecadiene -0.287 0.7744
## Concentration0.1:CompoundDecadiene -0.148 0.8821
## Concentration1:CompoundDecadiene -0.768 0.4436
## Concentration0.01:GroupPure compound -1.253 0.2117
## Concentration0.1:GroupPure compound -0.929 0.3542
## Concentration1:GroupPure compound -1.877 0.0621 .
## CompoundMenthone:GroupPure compound -1.848 0.0662 .
## CompoundAnethole:GroupPure compound -0.792 0.4291
## CompoundCineole:GroupPure compound -1.706 0.0896 .
## CompoundCarvone:GroupPure compound -0.792 0.4291
## CompoundDecadiene:GroupPure compound -0.016 0.9876
## Concentration0.01:CompoundMenthone:GroupPure compound 1.340 0.1819
## Concentration0.1:CompoundMenthone:GroupPure compound 1.169 0.2440
## Concentration1:CompoundMenthone:GroupPure compound 1.276 0.2036
## Concentration0.01:CompoundAnethole:GroupPure compound 0.226 0.8212
## Concentration0.1:CompoundAnethole:GroupPure compound 0.607 0.5448
## Concentration1:CompoundAnethole:GroupPure compound -0.200 0.8418
## Concentration0.01:CompoundCineole:GroupPure compound 0.662 0.5085
## Concentration0.1:CompoundCineole:GroupPure compound 0.761 0.4475
## Concentration1:CompoundCineole:GroupPure compound 1.531 0.1275
## Concentration0.01:CompoundCarvone:GroupPure compound 0.627 0.5316
## Concentration0.1:CompoundCarvone:GroupPure compound 0.140 0.8888
## Concentration1:CompoundCarvone:GroupPure compound 0.517 0.6060
## Concentration0.01:CompoundDecadiene:GroupPure compound 0.016 0.9875
## Concentration0.1:CompoundDecadiene:GroupPure compound 0.015 0.9883
## Concentration1:CompoundDecadiene:GroupPure compound 0.015 0.9883
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for quasipoisson family taken to be 1.304616)
##
## Null deviance: 532.90 on 239 degrees of freedom
## Residual deviance: 277.34 on 192 degrees of freedom
## AIC: NA
##
## Number of Fisher Scoring iterations: 14Anova(fit)## Analysis of Deviance Table (Type II tests)
##
## Response: Number
## LR Chisq Df Pr(>Chisq)
## Concentration 11.833 3 0.007978 **
## Compound 4.099 5 0.535248
## Group 150.730 1 < 2.2e-16 ***
## Concentration:Compound 10.497 15 0.787397
## Concentration:Group 4.883 3 0.180577
## Compound:Group 4.618 5 0.464205
## Concentration:Compound:Group 9.891 15 0.826546
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.