高级heatmap绘制ComplexHeatmap

ComplexHeatmap handbook
中文介绍
实例
我的简单一个例子

rm(list=ls())
suppressMessages(library(ComplexHeatmap))
suppressMessages(library(circlize))
suppressMessages(library(pheatmap))
suppressMessages(library(RColorBrewer))

pathway_data<-read.table("～/Modules_list/IPA/modules_all_IPA.txt",row.names = 1,sep = "\t",check.names = F,header = T)
nes<-read.csv("～/enrichment_nes.csv",check.names = F,header = T,row.names = 2)
padj<-read.csv("～/enrichment_padj.csv",check.names = F,header = T,row.names = 2)
precentage<-read.table("～/Modules_list/module_precentage.txt",sep="\t",row.names = 1,header =T )
precentage<-precentage[row.names(nes),]

ann<-data.frame(nes$Lob_Inflam,padj$Lob_Inflam)
row.names(ann)<-row.names(nes)
colnames(ann)<-c("NES","padj")
ann<-cbind(ann,precentage)

#define colors
col_fun1 = colorRamp2(c(10, 10, 250), c("#54C6DC", "black", "yellow"))
col_fun2 = colorRamp2(c(0, 100), c("white", "#E7298A"))
col_fun3 =colorRamp2(c(-3, 2.2), c("#BEBADA","#FB8072"))
  

col1 = colorRamp2(c(0, 5,15), c("navy", "white","firebrick3"))
col2=brewer.pal(5, "Set3")


pathway_data<-pathway_data[1:20,]

ha1 = HeatmapAnnotation(Novel_genes = anno_barplot(ann$nove_gene, height = unit(1.5, "cm"), 
                                          gp = gpar(fill = col2)))

ha2=HeatmapAnnotation(Known_transcripts = ann$known_transcripts,
Novel_transcripts = ann$novel_transcripts,
Lob_Inflam_NES=ann$NES,
col = list(Known_transcripts=col_fun1,Novel_transcripts=col_fun2,Lob_Inflam_NES=col_fun3),
height = unit(0.5, "cm"))



Heatmap(pathway_data, top_annotation = ha1,bottom_annotation = ha2,
            cluster_rows=T,cluster_columns = F,
            col=col1)

例子2

data_matrix<-data[,c(3,6)]

col_fun1 = colorRamp2(c(0,4), c("white", "#E7298A"))

ha=rowAnnotation(     Events=data$Feature_type,
                      Gene_type = data$Gene_type,
                      log_pvalue = data$`-log10(pvalue)`,
                      
                      col = list(Events=c("ES"="#D9D9D9","IR"="#BC80BD","ALT3"="#80B1D3","ALT5"="#FFED6F"),
                                 log_pvalue=col_fun1,
                                 Gene_type=c("lncRNA"= "#FFFFB3"  , "protein_coding"="#8DD3C7")))
#row_ha = rowAnnotation(log_pvalue = data$`-log10(pvalue)`,Gene_type = data$Gene_type)


col1 = colorRamp2(c(0, 0.4,1), c("navy", "white","firebrick3"))
#col1 = colorRamp2(c(0, 0.5,1), c("blue", "black","yellow"))
#col1 = colorRamp2(c(0,1), c("blue","yellow"))
Heatmap(data_matrix, right_annotation = ha,
        cluster_rows=T,cluster_columns = F,
        col=col1,border = F)