1. 用于展示大白菜和其他群体相似度、
输入文件：nearest.bins.lst.matrix
Bin1 Bin2 Value
Bin1000 CAtype 0
Bin1000 ChineseTP 0
Bin1000 EURtype 0
Bin1000 JPNtype 0
Bin1000 OilseedYN 0
Bin1000 PC 0
Bin1000 Taicai 1
Bin1000 sarson 0
Bin1001 CAtype 0
输入文件：sorted.groups.lst.added
Ordered Chr Type
Bin1 A01 GenomicSequence
Bin2 A01 GenomicSequence
Bin3 A01 GenomicSequence
Bin4 A01 GenomicSequence
Bin5 A01 GenomicSequence
Bin6 A01 GenomicSequence
Bin7 A01 GenomicSequence
library(ggplot2)
library(patchwork)
mytheme2 <- theme_bw() + theme(legend.title=element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
#axis.title.y = element_text(size=8,angle=90),
#axis.text.x=element_text(size=6,angle=0),
axis.text.x= element_blank(),
axis.ticks.x = element_blank(),
axis.text.y = element_text(size=8), ##- biao qian
#axis.text.y = element_blank(),
#axis.ticks.y = element_blank(), ##- ke du xian
legend.position="none",
legend.key.size = unit(0.4,'cm'),
legend.text = element_text(size=6,angle=0),
strip.text = element_text(size=4)
)
#argv<-commandArgs(TRUE)
data <- read.table("nearest.bins.lst.matrix", header = TRUE, sep="\t") ##- nearest.bins.lst.matrix
group <- read.table("sorted.groups.lst.added", header = TRUE, sep="\t") ##- sorted.groups.lst
orderBin <- factor(group$Ordered)
data$Bin1 <- factor(data$Bin1, levels=orderBin)
data$Bin2 <- factor(data$Bin2, levels=c("Taicai", "ChineseTP", "PC", "sarson", "JPNtype", "EURtype", "OilseedYN", "CAtype"))
group$Ordered <- factor(group$Ordered, levels=orderBin)
p1 <- ggplot(data, aes(x=Bin1, y=Bin2, fill=Value, color=Value)) +
geom_tile() +
scale_colour_gradient(low = "white", high = "red") +
scale_fill_gradient(low = "white", high = "red") +
mytheme2
p2 <- ggplot(group, aes(x=Ordered, y=1, fill=Type, color=Type)) +
geom_tile(color="white") +
theme_bw() +
scale_fill_manual(values=c("#ef476f", "#ffd166", "#06d6a0", "#118ab2", "#ffbe0b", "#fb5607", "#ff006e", "#8338ec", "#3a86ff", "#a8dadc")) +
#scale_fill_brewer(palette = "Paired") +
theme(legend.title=element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
#axis.title.y = element_text(size=8,angle=90),
#axis.text.x=element_text(size=6,angle=0),
axis.text.x= element_blank(),
axis.ticks.x = element_blank(),
#axis.text.y = element_text(size=6), ##- biao qian
axis.text.y = element_blank(),
axis.ticks.y = element_blank(), ##- ke du xian
legend.position="none",
legend.key.size = unit(0.4,'cm'),
legend.text = element_text(size=6,angle=0),
strip.text = element_text(size=4)
)
p <- p1 / p2 + plot_layout(heights = c(30, 1))
ggsave(file="aa.pdf", plot=p, width = 12, height = 3)
结果图：
大白菜与其他群体相似度-01.jpg
