ComplexHeatmap 实战
参数介绍里面很丰富，但具体细节可能需要多做几张图才能慢慢体会！
下载及练习使用的矩阵在下面代码：
代码语言：txt复制#下载可以通过GitHub和biocmanage两种，前者最新版本，后者稳定版本library(devtools)install_github("jokergoo/ComplexHeatmap")sessionInfo()library(ComplexHeatmap)#这个矩阵是官方document提供的set.seed(123)nr1 = 4; nr2 = 8; nr3 = 6; nr = nr1 nr2 nr3nc1 = 6; nc2 = 8; nc3 = 10; nc = nc1 nc2 nc3mat = cbind(rbind(matrix(rnorm(nr1*nc1, mean = 1, sd = 0.5), nr = nr1), matrix(rnorm(nr2*nc1, mean = 0, sd = 0.5), nr = nr2), matrix(rnorm(nr3*nc1, mean = 0, sd = 0.5), nr = nr3)), rbind(matrix(rnorm(nr1*nc2, mean = 0, sd = 0.5), nr = nr1), matrix(rnorm(nr2*nc2, mean = 1, sd = 0.5), nr = nr2), matrix(rnorm(nr3*nc2, mean = 0, sd = 0.5), nr = nr3)), rbind(matrix(rnorm(nr1*nc3, mean = 0.5, sd = 0.5), nr = nr1), matrix(rnorm(nr2*nc3, mean = 0.5, sd = 0.5), nr = nr2), matrix(rnorm(nr3*nc3, mean = 1, sd = 0.5), nr = nr3)))mat = mat[sample(nr, nr), sample(nc, nc)] # random shuffle rows and columnsrownames(mat) = paste0("row", seq_len(nr))colnames(mat) = paste0("column", seq_len(nc))第一部分 Heatmap函数
直接实战来认识参数
图一涉及到颜色，标题，分版块等
图一
代码展示
代码语言：txt复制Heatmap(mat, name = "mat", col=colorRamp2(c(-2,0,2),c('skyblue2','white','red3')), #颜色设置 color_space = "RGB", border = T, cluster_columns = F, cluster_rows = F, row_order=NULL, column_order=NULL, column_title_side = "bottom", #设置行名及列名具体格式 column_title_gp = gpar(fontsize=13,fondface="bold"), row_title_gp = gpar(fontsize=13,fondface="bold"), row_split = factor(c(rep(c("gene A","gene B","gene C"),time= c(4,6,8))), #根据行列分版块 levels = c("gene A","gene B","gene C")), column_split = factor(c(rep(c("low risk","high risk"),12)), levels =c("low risk","high risk"), labels = c("low risk","high risk")), show_column_names = F)第二部分 Annotation
注释主要用到 HeatmapAnnotation 这个参数，参数使用直接上图来体会
图二涉及到注释
图二
代码语言：txt复制#图二Heatmap(matrix(rnorm(100), 10), col = colorRamp2(c(-2,0,2),c("skyblue","white","red3")), show_row_names = F, row_split = rep(c("model 1","model 2","model3"),time=c(2,3,5)), row_title_gp = gpar(fontsize=14,fontface='bold'), top_annotation = HeatmapAnnotation(foo = anno_block(gp = gpar(fill = 2:4), labels = c("group1", "group2", "group3"), labels_gp = gpar(col = "white", fontsize = 10))), cluster_rows = F, cluster_columns = F, column_split = rep(1:3,time=c(2,3,5)), show_column_names = F)·
简单认识参数之后，那就开始吧，实战一
实战一
中的一张简单的热图，热图中5中signature在不同分组 中的表达，注释文件时是
实战一
.
一个小时搞定
实战一
代码如下：
代码语言：txt复制mat <- matrix(rnorm(500),nrow = 5)colnames(mat) <- paste0("sample",1:100)rownames(mat) <- paste0("signature",c(1,16,3,2,13))cli <- data.frame(Tobacoo=sample(c("No","Yes"),100,replace = T), Alchoal=sample(c("No","Yes"),100,replace = T), HPV16=c(sample(c("No","Yes"),30,replace = T),rep("No",20),rep("Yes",30),rep("No",20)), cluster=rep(c("A","B","C1","C2"),time=c(20,30,30,20)))cli$Tobacoo <- factor(cli$Tobacoo)Tobacoo <- c(pal_nejm()(8)[1],pal_nejm()(8)[2])names(Tobacoo) <- c("Yes","No")cli$Alchoal <- factor(cli$Alchoal)Alchoal <- c(pal_nejm()(8)[1],pal_nejm()(8)[2])names(Alchoal) <-c("Yes","No")cli$HPV16 <- factor(cli$HPV16)HPV16<- c(pal_nejm()(8)[1],pal_nejm()(8)[2])names(HPV16)<- c("Yes","No")cli$cluster <- factor(cli$cluster)cluster <- c(pal_nejm()(8)[3],pal_nejm()(8)[4],pal_nejm()(8)[5],pal_nejm()(8)[6])names(cluster) <- c("A","B","C1","C2")library(ComplexHeatmap)library(circlize)library(ggsci)Heatmap(mat,col = colorRamp2(c(-2,0,2),c("skyblue2","white","red2")), color_space = "RGB", column_split = factor(rep(c("A","B","C"),time=c(20,30,50))), cluster_columns = F, show_column_names = F, top_annotation = HeatmapAnnotation( Tobacoo=cli$Tobacoo, Alchoal=cli$Alchoal, HPV16=cli$HPV16, cluster=cli$cluster, annotation_legend_param=list(labels_gp = gpar(fontsize = 9), title_gp = gpar(fontsize = 9, fontface = "bold"), ncol=1), col = list(Tobacoo=Tobacoo, Alchoal=Alchoal, HPV16=HPV16, cluster=cluster), show_annotation_name = TRUE, annotation_name_side="right", annotation_name_gp = gpar(fontsize = 9, fontface = "bold")))
