Cell同款 | 配色热图篇

Cell同款 | 配色热图篇 by 在生信的坑里挖呀挖呀挖

Cell同款 | 配色热图篇

之前画过2次热图啦，Cancer Cell同款 | 热图 和 Molecular Therapy同款 | 热图。学会了画热图，再看下画啥样的热图，今天就以发在Cell上的Figure为例，都是Cell里的热图噢，果然配色很常见，样式很典型。至此想必热图的门道就摸出来了吧。

Cell上的示例图1

Figure 5. Differential expression of the top 45 AD GWAS genes across all major CSF immune cell types

简单画个热图展示下

配色ex_color = c("#6238ff","#ffffff","#ff220e")。

绘制热图的简单脚本如下。

library(pheatmap)df <- read.delim("test.txt",header=T,row.names=1,sep='\t',stringsAsFactors = FALSE,  check.names = FALSE,quote = "")ex_color = c("#6238ff","#ffffff","#ff220e")pdf("test.pdf",height = 5, width = 4)
p <- pheatmap(df,   scale="row",   cluster_col=FALSE,   cluster_rows=TRUE,   show_rownames=FALSE,   show_colnames=TRUE,   border_color=NA,   col = colorRampPalette(ex_color)(100))
print(p)dev.off()

其中test.txt示例如下，行为基因，列为样本的表达量矩阵。

Cell上的示例图2

Figure 2.(B) Heatmap displaying expressions of marker genes for each T cell cluster.

图2-4的配色就不给大家提取了，需要的话可以看顶刊文献千千万，Figure配色随便拾，展示下，知道顶刊里的热图都长啥样，之后照着画！

Cell上的示例图3

Figure 4(I) Heatmap of individual genes from leading-edge Hallmark angiogenesis pathway stratified by brain tissue type and PBN/TAN.

Cell上的示例图4

Figure 5(A) Heatmap of volume-normalized cortical layer distribution of GABAergic cell types

Cell上的示例图5

Figure 5(K) Expression levels of neurotransmitter and neuromodulator receptor subunit and transporter genes in PV or SST neurons along the hierarchical level in visual (left) and somatosensory (right) systems.

Cell上的示例图6

Figure 2. (B and C) Top DEGs (B) and DEPs (C) between cell types.

Cell上的示例图7

对了这个配色可以用library(viridis)里的scale_fill_viridis(option = "D")

Figure 2. (D) HD TF expression across cell/tissue types with Coordinator enrichment. Colored circles correspond to the schematic and data in (C).

参考文献

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