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