我有一个像这样的数据框:
gene s1 s2 s3
1 -3.83 -8.17 -8.59
2 0.33 -4.51 -7.27
3 0.15 -5.26 -6.2
4 -0.08 -6.13 -5.95
5 -1.15 -4.82 -5.75
6 -0.99 -4.11 -4.85
7 0.42 -4.18 -4.54
8 -0.32 -3.43 -4.4
9 -0.72 -3.37 -4.39
我想使用pheatmap制作一个热图,如果它低于-4,则应为绿色,而超过+4的则应为红色,而介于两者之间的则应为红色/绿色。我也不想扩展我的数据并且没有聚类。到目前为止,我在R中有此代码:
d <- read.table("test.txt", header = TRUE, sep = "\t", row.names = 1, quote = "")
pheatmap(as.matrix(d), # matrix
scale = "none", # z score scaling applied to rows
cluster_cols=FALSE, # do not cluster columns
cluster_rows = FALSE,
treeheight_row=0, # do not show row dendrogram
show_rownames=FALSE, # do not show row names i.e gene names
main = "test.txt",
color = colorRampPalette(c("#0016DB","#FFFFFF","#FFFF00"))(50),
)
如何使用上面提到的配色方案绘制此图。
谢谢
答案 0 :(得分:1)
d <-read.table(text="gene s1 s2 s3
1 -3.83 -8.17 -8.59
2 0.33 -4.51 -7.27
3 0.15 -5.26 -6.20
4 -0.08 -6.13 -5.95
5 -1.15 -4.82 -5.75
6 -0.99 -4.11 -4.85
7 0.42 -4.18 -4.54
8 -0.32 -3.43 -4.40
9 -0.72 -3.37 -4.39", header=T)
library(pheatmap)
my_colors <- c(min(d),seq(-4,4,by=0.01),max(d))
my_palette <- c("green",colorRampPalette(colors = c("green", "red"))
(n = length(my_colors)-2), "red")
pheatmap(as.matrix(d),
scale = "none",
cluster_cols=FALSE,
cluster_rows = FALSE,
treeheight_row=0,
show_rownames=FALSE,
main = "test.txt",
color = my_palette,
breaks = my_colors)
由reprex package(v0.3.0)于2019-05-29创建