pheatmap 与 complexheatmap

#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 + nr3

nc1 = 6; nc2 = 8; nc3 = 10; nc = nc1 + nc2 + nc3

mat = 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 columns

rownames(mat) = paste0("row", seq_len(nr))

colnames(mat) = paste0("column", seq_len(nc))

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)

#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)

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")))