R语言热图笔记

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背景知识

pheatmap包

代码如下所示：

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# 1. Set working directory 
rm(list=ls())
temp_path <- file.path("D:","heatmap_temp_for_rna_seq")
dir.create(temp_path)
setwd(temp_path)
getwd()
# 2. Load raw data
# This raw data was generated randomly
raw_data <- read.delim("https://raw.githubusercontent.com/20170505a/raw_data/master/heatmap_raw_data.csv",header=T,sep=",")
head(raw_data)
str(raw_data)
# 3. Transform raw data(data.frame) into matrix
raw_data_matrix <- as.matrix(raw_data[-1])
rownames(raw_data_matrix) <- raw_data[,1]
# 4. pheatmap package
# first R packages: pheatmap
library(pheatmap)
pheatmap(raw_data_matrix,
         border=NA,border_color=NA,
         color = colorRampPalette(c("blue","white","red"))(100),
         cellwidth = 36,cellheight = 8,
         cluster_rows = T,cluster_cols = F,
         #cutree_rows = 4,
         fontsize = 8, 
         scale="row",
         show_rownames=T
         # ，filename = "pheatmap_R_package_heatmap.pdf"
         )

参考资料

  1. 如何画热图.Tang Boyun.知乎专栏