通常,在R的pheatmap中显示行标签是没有问题的。但是,请参阅我有一些复杂的行标签,它们是将一个字符串的开头和另一个字符串的结尾组合在一起的字符串。例如,“ ABC **** 123”。
这是一个示例和我的代码:
library(pheatmap)
library(stringr)
# create an example
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")
# make random pvalue to show at the end of rownames
random.pvalue <- formatC(runif(n = 20,min = 0.0000000000001,max = 0.00000000001),format = "e",
digits = 2)
# creat new rownames with fixed width
add.label <- paste0(str_pad(rownames(test),
width=12,
side="right"),
random.pvalue)
rownames(test) <- add.label # update rownames
# Draw heatmaps
pheatmap(test) # you could see the pvalues are not aligned
相信我,我通过在R中使用formatC()和str_pad()来将这些行标签强制固定为宽度。但是,当我对这些行标签使用pheatmap时,标签并没有按照我的想象显示,它们像然后,您可以清楚地看到即使行标签具有相同的字符串宽度,行标签也未对齐。
[1] "Gene1 7.77e-12" "Gene2 2.67e-12" "Gene3 8.67e-12" "Gene4 6.61e-12"
[5] "Gene5 2.36e-12" "Gene6 3.09e-12" "Gene7 5.44e-12" "Gene8 3.18e-13"
[9] "Gene9 1.34e-12" "Gene10 4.52e-12" "Gene11 2.03e-12" "Gene12 5.31e-12"
[13] "Gene13 9.66e-12" "Gene14 9.02e-12" "Gene15 2.91e-13" "Gene16 7.37e-13"
[17] "Gene17 7.95e-12" "Gene18 8.04e-12" "Gene19 8.31e-12" "Gene20 9.94e-12"
也许有人可以用一个简单的例子来教我如何解决这个问题。
非常感谢!
您可以使用固定字体(不是比例字体):
library(pheatmap)
library(grid)
library(stringr)
mat <- mtcars[1:10,1:6]
rn <- stringr::str_pad(rownames(mat), max(nchar(rownames(mat))), side = "right")
p <- signif(1e-9*mat[,4], digits = 4)
pheatmap::pheatmap(as.matrix(mtcars[1:10,1:6]), scale="column",
labels_row=paste(rn, p, sep=" "), fontfamily = "mono")
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