heatmap相关

===========================heatmap2工具========================
data <- read.csv("cluster_expression.txt",header = TRUE,sep = "\t",fill = TRUE)

row.names(data) <- data$Name

data <- data[,2:length(data[1,])]

data_matrix <- data.matrix(data)

data_nor <- normalize.quantiles(data_matrix)

jpeg("heatmap.jpeg",width = 1200, height = 1200,res = 144)

col = colorpanel(80, low ="white" , high = "darkblue")

heatmap.2(data_matrix,Colv = FALSE, Rowv=FALSE ,col = col,margins = c(12,12),dendrogram="none",trace = "none",keysize = (1),density.info = "none")

heatmap.2(data_matrix,col=bluered,scale="row",trace = "none",keysize = 1,labRow=NA,cexCol=1.3,srtCol=45,Colv = FALSE,dendrogram="row")

dev.off()

=============pheatmap工具===================================

data <- read.table("RNAseq.nicotine.txt",header=T,sep="\t")

row.names(data) <- data$Sample

data <- data[,2:length(data[1,])]

pheatmap(data, color = colorRampPalette(c("navy", "white", "firebrick3"))(50),fontsize = 10,border_color=FALSE,scale="row")

pheatmap(data, color = colorRampPalette(c("navy", "white", "firebrick3"))(50),fontsize = 5,border_color=FALSE,cutree_rows=5,filename="RNAseq.heatmap.pdf")

bk <- c(seq(-3,-0.01,by=0.01),seq(0,3,by=0.01))

pheatmap(data, color = c(colorRampPalette(colors = c("blue","white"))(length(bk)/2),colorRampPalette(colors = c("white","red"))(length(bk)/2)),legend_breaks=seq(-3,3,1),breaks=bk,fontsize = 8,border_color=FALSE,cluster_cols=FALSE)

pheatmap(data, color = c(colorRampPalette(colors = c("blue","white"))(length(bk)/2),colorRampPalette(colors = c("white","red"))

(length(bk)/2)),legend_breaks=seq(-3,3,1),breaks=bk,fontsize = 8,border_color=FALSE,cluster_cols=FALSE,filename="known.miRNA.heatmap.pdf",cutree=5)