我正在尝试在网格中绘制多个热图，并希望基于所有热图的0到最大值来获得热颜色，以便热图例在几个热图之间具有可比性且具有相同的范围颜色传说中的热量。由于必须为所提供的任何数据矩阵完成，这里是Rscript，我到目前为止创建热图，同时还将单个热图的最大值限制为99百分位，这是我需要保留的另一个要求。所以，我最终会在将每个热图上限到99％之后查看最大值。请建议我如何实现类似的热量缩放。
start.time <- Sys.time()
options(echo=F) # if you want see commands in output file
setwd("./")
args <- commandArgs(trailingOnly = TRUE)
numArgs<-length(args)
print(numArgs-2)
if(args[1] == "-h"){
writeLines("\nTo run : Rscript readDensity_heatmap.R <base name of tag dir folder> <sample 1> <sample 2>")
writeLines("e.g Rscript readDensity_heatmap.R Peaks <dataMatrix1 dataMatrix2 .......\n")
stop("", call.=F)
writeLines("\n")
}else if(numArgs < 3){
stop("Please supply 3 arguments")
}
library(pheatmap)
library(gplots)
library(reshape2)
library(fields)
z=3
for (i in 1:as.integer(args[2])){
eqn<-paste("cond", i, '<-colsplit("', args[z], '", "_",', 'c("a", "b" ))', sep="" )
eval(parse(text=eqn))
z=z+1
}
var_names <- paste("file", 1:(numArgs-1), sep="")
df_names <- paste("df", 1:(numArgs-1), sep="")
d=1
j=3
prefix<-args[1]
pdf(paste0(prefix, "_readDensityHeatmap_TFs.pdf"), height=20, width=10)
par(mfrow=c(10,3))
par(mar=c(3,3,3,3))
for (i in 1:(numArgs-2)){
var_names[d]=paste("HeatMatrix/", prefix, "_", args[j], "_HeatMatrix.txt", sep="")
if (!file.exists(var_names[d]) ){
writeLines(paste('"', var_names[d], '"', "not present\n", sep=" "))
stop(" ")
}
lhs<-df_names[d]
rhs<-paste('read.delim("', var_names[d], '"' , ",header=T, sep='\t')", sep="")
dfEqn=paste(lhs, "<-", rhs, sep="")
eval(parse(text=dfEqn))
eqn<-paste0("x<-df", d)
eval(parse(text=eqn))
x<-x[,-1]
x<-x[order(rowMeans(x)),]
quantile.range <- quantile(as.matrix(x), probs = seq(0, 1, 0.01))
palette.breaks <- seq(quantile.range["0%"], quantile.range["99%"], .001)
mycol <- colorpanel(n=length(palette.breaks)-1,low="white",mid="blue",high="red")
eqn<-paste0("cond<-cond", d, "$a" ) #
eval(parse(text=eqn))
eqn<-paste0("condp2<-cond", d, "$b" ) #
eval(parse(text=eqn))
image(as.matrix(t(x)), col=mycol,breaks=palette.breaks, xaxt="n", yaxt="n", axes=F, main=paste(cond, condp2, sep=" ") )
mtext(text=c(-2000, 0, 2000), side=1, line=0.3, at=c(0, 0.5, 1), las=1, cex=0.8)
image.plot(as.matrix(t(x)), col=mycol,breaks=palette.breaks,legend.only=T )
d=d+1
j=j+1
}
########################
dev.off()
end.time <- Sys.time()
time.taken <- end.time-start.time
time.taken
编辑：样本文件。在峰值中心周围只有50列（400个），只有几十行中的10列。根据提供给脚本的第一，第二和第三个参数，读取几个这样的文件。第一个参数提供文件的基本名称，2nd表示从第二个参数后面的名称中读取的文件数量（这些文件可以是用户想要提供的数量）
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