rm(list = ls())
library(openxlsx)
library(dplyr)
##
## 载入程辑包：'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(tidyr)
library(ggdendro)
library(ggplot2)
dir_path <- "C:\\Users\\liyix\\OneDrive\\Desktop\\"
dir_path_name <- list.files(pattern = ".*xlsx",dir_path,full.names = T, recursive = F)
#dir_path_name
#getSheetNames(grep("data.xlsx",dir_path_name,value = T))
data_1 <- read.xlsx(grep("data.xlsx",dir_path_name,value = T),sheet = 1)
##View(Guide)
#dim(data_1) #[1] 139 9
#head(data_1)
data_1 <- data_1[1:26,]
data_1$Feature <- NULL
colnames(data_1) <- LETTERS[1:ncol(data_1)]
row.names(data_1) <- letters
#View(data_1)
###########################################################dendro_1_LEFT
data_2 <- data_1
##########################
#str(data_2)
#View(data_2)
head(data_2)
## A B C D E F G H
## a -9.00 -7.00 -5.00 7.33 0 0 1 1
## b 0.00 8.33 -3.00 1.33 0 0 0 1
## c -2.67 0.00 -2.08 4.67 1 2 2 1
## d -9.00 2.00 -1.33 0.00 0 1 1 1
## e NA NA -1.33 2.00 0 0 0 0
## f -9.00 0.00 -1.17 4.17 1 1 1 2
##########################
#data_2[is.na(data_2)] <- 0
dd <- dist(scale(data_2), method = "euclidean")
hc <- hclust(dd, method = "complete")
ggdendrogram(hc, rotate = T)
##############################
dend <- as.dendrogram(hc)
dendata <- dendro_data(dend,type = "rectangle")
#add column family to labs dataframe (look like VLOOKUP in excel)
labs <- label(dendata)
###########################################plot
data_plot <- segment(dendata)
labs$y <- -0.1
#head(labs)
#head(data_plot)
#dim(data_2)
p <- ggplot(data_plot) +
geom_segment(aes(x=x, y=y, xend=xend, yend=yend, color=""),size = .1) +
coord_flip() +
#geom_text(data=labs,size= 1,
# aes(label=label, x=x, y= y),vjust = 0.5,hjust = 0, color = "white")+
geom_segment(data=labs,aes(x=x, y=y, xend=x, yend=0, color=""),size = .1) +
scale_colour_manual(values = c("black")) +
scale_x_continuous(expand = c(0,0),limits = c(0.5,nrow(data_2)+0.5)) +
scale_y_reverse(expand = c(0.01, 0.01))
p_dendro <- p + theme(legend.position = "none")+
theme(axis.line = element_blank())
p_dendro
#####################################################################denfdro_2_TOP
#data_2[is.na(data_2)] <- 0
data_4 <- data.frame(t(data_2))
#View(data_4)
dd1 <- dist(scale(data_4), method = "euclidean")
hc1 <- hclust(dd1, method = "complete")
ggdendrogram(hc1, rotate = T)
##############################
dend1 <- as.dendrogram(hc1)
dendata1 <- dendro_data(dend1,type = "rectangle")
#add column family to labs dataframe (look like VLOOKUP in excel)
labs1 <- label(dendata1)
data_plot1 <- segment(dendata1)
#labs1$y <- -0.2
head(labs1)
## x y label
## 1 1 0 A
## 2 2 0 B
## 3 3 0 D
## 4 4 0 C
## 5 5 0 E
## 6 6 0 F
head(data_plot1)
## x y xend yend
## 1 2.53125 10.995791 1.0000 10.995791
## 2 1.00000 10.995791 1.0000 0.000000
## 3 2.53125 10.995791 4.0625 10.995791
## 4 4.06250 10.995791 4.0625 7.784358
## 5 4.06250 7.784358 2.5000 7.784358
## 6 2.50000 7.784358 2.5000 5.979765
p1 <- ggplot(data_plot1) +
geom_segment(aes(x=x, y=y, xend=xend, yend=yend, color=""),size = 0.1) +
# geom_segment(data=labs1,size= 3,
# aes(x=x, y= y, xend = x, yend = 0), color = "green") +
scale_colour_manual(values = c("black")) +
scale_x_continuous(expand = c(0, 0), limits = c(0.5,ncol(data_2) + 0.5)) +
scale_y_continuous(expand = c(0, 0))
p_dendro1 <- p1 + theme(legend.position = "none")+
theme(axis.line = element_blank()) #+
# labs(x = "", y = "", title = "")
#theme(panel.background = element_rect(fill = NA, colour = NA),
# plot.background = element_rect(fill = NA,colour = NA))
p_dendro1
##################################################2___HM-P-VALUE
#colnames(data_1)
data_21 <- data_1
#View(data_21)
data_21$num <- row.names(data_21)
data_3 <- gather(data_21, key = key, value = value, -num)
head(data_3)
## num key value
## 1 a A -9.00
## 2 b A 0.00
## 3 c A -2.67
## 4 d A -9.00
## 5 e A NA
## 6 f A -9.00
data_3$num <- factor(data_3$num, levels = unique(labs$label))
#data_3$key <- gsub("\\."," ", data_3$key)
data_3$key <- factor(data_3$key, levels = unique(labs1$label))
#data_3$A
#unique(data_3$key)
p2 <- ggplot() + geom_tile(data = data_3,aes( x = key,
y= num,
height = 1,
fill = value,
width = 1, colour= ""),size= 0.2) +
ylab("") + xlab("") +
theme(legend.position = c(1.22,0.81),
plot.background = element_rect(fill="green")) +
scale_y_discrete(expand = c(0, 0),position = "right") +
scale_x_discrete(expand = c(0, 0)) +
scale_fill_gradient2(low="blue", high="red",
name = expression('Value'), na.value="gray90")
p_pvalue <- p2 + guides(colour = guide_legend("Missing value", override.aes = list(fill="gray90"))) +
theme(axis.text.x = element_text(angle = 90, vjust = 0.3, hjust = 1, color = "black")) +
scale_colour_manual(values= "gray80") +
theme(axis.ticks = element_blank(),
axis.text.y = element_blank(),
#panel.background = element_blank(),
legend.key.height = unit(0.8,"line"),
legend.key.width = unit(0.7,"line"))
#theme(panel.background = element_rect(fill = NA, colour = NA),
# plot.background = element_rect(fill = NA,colour = NA))
p_pvalue
##################################################6___MERGE
library(patchwork)
plot_spacer() + p_dendro1 + p_dendro + p_pvalue +
plot_layout(widths = c(1,2),
heights = c(0.2,2), guides = 'collect')
#################################################################
(plot_spacer() + theme(axis.text = element_blank(),
axis.title = element_blank(),
axis.ticks = element_blank(),
plot.margin = unit(c(0,0,0,0), "cm"),
plot.background = element_rect(fill="green"))) +
(p_dendro1 + theme(axis.text = element_blank(),
axis.title = element_blank(),
axis.ticks.x = element_line(color= "red"),
axis.ticks.length.x = unit(2, "mm"),
axis.ticks.y = element_blank(),
panel.background=element_rect(fill="red"),
panel.grid=element_blank(),
axis.ticks.length.y = unit(0, "mm"),
plot.background = element_rect(fill="green"),
plot.margin = unit(c(0,3,0,0), "cm"))) +
(p_dendro + theme(axis.text = element_blank(),
axis.title = element_blank(),
axis.ticks = element_blank(),
panel.background=element_rect(fill="yellow"),
plot.background = element_rect(fill="blue"),
panel.grid=element_blank(),
plot.margin = unit(c(0,0,0,0), "cm"))) +
(p_pvalue + theme(axis.text = element_blank(),
axis.title = element_blank(),
axis.ticks = element_blank(),
axis.ticks.y = element_blank(),
axis.ticks.length.y = unit(0, "mm"),
panel.background=element_rect(fill="red"),
plot.background = element_rect(fill="green"),
plot.margin = unit(c(0,3,0,0), "cm"))) +
plot_layout(widths = c(1,2),
heights = c(0.2,5), guides = 'auto') +
theme(legend.position=c(1.2,0.85))
####################################################
ggsave(filename = paste0(Sys.Date(),"-plot_dendro_11.tif"),
plot = last_plot(), device = "tiff", path = dir_path,
width = 15, height = 18, units = "cm",
dpi = 300, limitsize = TRUE)
ggsave(filename = paste0(Sys.Date(),"-plot_hm-dendro_all.pdf"),
plot = last_plot(), device = "pdf", path = dir_path,
width = 16, height = 18, units = "cm",
dpi = 300, limitsize = TRUE)
###########################################
write.csv(labs, paste0(dir_path,Sys.Date(),"-","labs_order.csv"),row.names = FALSE,na = "")