不知道你用的是什么脚本, 如果贴一下代码,我可以告诉你怎么修改代码;

再R语言里面对数转换很简单:  log2(x)

library("argparse")

parser <- ArgumentParser(description='plot geneExp heatmap')

parser$add_argument( "-i", "--input", type="character",required=T,

help="input gene expreesion matrix data ,[required]",

metavar="filepath")

parser$add_argument("-s", "--showrownames", action='store_true',

help="whether show  rownames [optional, default: False]")

parser$add_argument( "-c", "--color", type="character",nargs='+',required=F,default=c("blue", "white", "red"),

help="color map of heatmap, give three color [default=c('blue', 'white', 'red')",

metavar="color")

parser$add_argument( "-o", "--outdir", type="character", default=getwd(),

help="output file directory [default cwd]",

metavar="outdir")

parser$add_argument("-n", "--name", type="character", default="heatmap",

help="out file name prefix [default heatmap]",

metavar="prefix")

parser$add_argument( "-H", "--height", type="double", default=8,

help="the height of pic   inches  [default 8]",

metavar="height")

parser$add_argument("-W", "--width", type="double", default=5,

help="the width of pic   inches [default 5]",

metavar="width")

opt <- parser$parse_args()

if( !file.exists(opt$outdir) ){

if( !dir.create(opt$outdir, showWarnings = FALSE, recursive = TRUE) ){

stop(paste("dir.create failed: outdir=",opt$outdir,sep=""))

}

}

library(pheatmap)

#-----------------------------------------------------------------

# reading data

#-----------------------------------------------------------------

df<-read.table(opt$input,sep="\t",row.names=1,header = TRUE,check.names=FALSE,comment.char="")

#去除表达量全为零的行

if(sum(rowSums(df)==0)>0){

print(c("去除在所有的样本中表达量都为0的基因:",rownames(df)[rowSums(df)==0]))

df=df[rowSums(df)!=0,]

}

color_map<-colorRampPalette(opt$color)(100)

#更多热图参数调整见：https://www.omicsclass.com/article/1162

df=log2(df)

pdf(file=paste(opt$outdir,"/",opt$name,".pdf",sep=""), height=opt$height, width=opt$width)

pheatmap(df,color=color_map,border=FALSE, 

scale="row",

show_colnames=TRUE,

show_rownames=opt$showrownames

)

dev.off()

png(filename=paste(opt$outdir,"/",opt$name,".png",sep=""), height=opt$height*300, width=opt$width*300, res=300, units="px")

pheatmap(df,color=color_map,border=FALSE, 

scale="row",

show_rownames=opt$showrownames,

show_colnames=TRUE)

dev.off()