R heatmap.2 手动分组行和列

Question

这个问题在这里已经有了答案:





How to create pre-annotated rowside column in heatmap.2

(2 个回答)


4年前关闭。




我有以下 MWE，我在其中制作了一个热图，而没有执行任何聚类和显示任何树状图。我想以比现在更好看的方式将我的行(基因)按类别分组在一起。

这是 MWE:

#MWE
library(gplots)
mymat <- matrix(rexp(600, rate=.1), ncol=12)
colnames(mymat) <- c(rep("treatment_1", 3), rep("treatment_2", 3), rep("treatment_3", 3), rep("treatment_4", 3))
rownames(mymat) <- paste("gene", 1:dim(mymat)[1], sep="_")
rownames(mymat) <- paste(rownames(mymat), c(rep("CATEGORY_1", 10), rep("CATEGORY_2", 10), rep("CATEGORY_3", 10), rep("CATEGORY_4", 10), rep("CATEGORY_5", 10)), sep=" --- ")
mymat #50x12 MATRIX. 50 GENES IN 5 CATEGORIES, ACROSS 4 TREATMENTS WITH 3 REPLICATES EACH
png(filename="TEST.png", height=800, width=600)
print(
heatmap.2(mymat, col=greenred(75),
      trace="none",
      keysize=1,
      margins=c(8,14),
      scale="row",
      dendrogram="none",
      Colv = FALSE,
      Rowv = FALSE,
      cexRow=0.5 + 1/log10(dim(mymat)[1]),
      cexCol=1.25,
      main="Genes grouped by categories")
)
dev.off()

产生这个:



我想将行中的 CATEGORIES 组合在一起(如果可能的话，也可以将列中的处理组合在一起)，所以它看起来像下面这样:



或者，也许更好，使用左侧的 CATEGORIES，与执行聚类并显示树状图时的方式相同；然而更容易和更清晰......

有什么办法吗？谢谢!!

编辑!!

我在评论中了解到 RowSideColors，我在下面制作了 MWE。但是，我似乎无法在输出 png 中打印图例，加上图例中的颜色不正确，我也无法正确定位。因此，请帮助我了解下面 MWE 中的图例。

另一方面，我使用由 12 种颜色组成的调色板“Set3”，但是如果我需要 12 种以上的颜色(如果我有 12 种以上的类别)怎么办？

新 MWE

library(gplots)
library(RColorBrewer)
col1 <- brewer.pal(12, "Set3")
mymat <- matrix(rexp(600, rate=.1), ncol=12)
colnames(mymat) <- c(rep("treatment_1", 3), rep("treatment_2", 3), rep("treatment_3", 3), rep("treatment_4", 3))
rownames(mymat) <- paste("gene", 1:dim(mymat)[1], sep="_")
mymat
mydf <- data.frame(gene=paste("gene", 1:dim(mymat)[1], sep="_"), category=c(rep("CATEGORY_1", 10), rep("CATEGORY_2", 10), rep("CATEGORY_3", 10), rep("CATEGORY_4", 10), rep("CATEGORY_5", 10)))
mydf
png(filename="TEST.png", height=800, width=600)
print(
    heatmap.2(mymat, col=greenred(75),
              trace="none",
              keysize=1,
              margins=c(8,6),
              scale="row",
              dendrogram="none",
              Colv = FALSE,
              Rowv = FALSE,
              cexRow=0.5 + 1/log10(dim(mymat)[1]),
              cexCol=1.25,
              main="Genes grouped by categories",
              RowSideColors=col1[as.numeric(mydf$category)]
              )
    #THE LEGEND DOESN'T WORK INSIDE print(), AND THE POSITION AND COLORS ARE WRONG
    #legend("topright",
    #       legend = unique(mydf$category),
    #       col = col1[as.numeric(mydf$category)],
    #       lty= 1,
    #       lwd = 5,
    #       cex=.7
    #       )
)
dev.off()

其中产生:



请帮我看一下图例，假设情况下我需要 12 种以上的颜色。谢谢!

Answer 1

我会使用 pheatmap 包。你的例子看起来像这样:

library(pheatmap)
library(RColorBrewer)

# Generte data (modified the mydf slightly)
col1 <- brewer.pal(12, "Set3")
mymat <- matrix(rexp(600, rate=.1), ncol=12)
colnames(mymat) <- c(rep("treatment_1", 3), rep("treatment_2", 3), rep("treatment_3", 3), rep("treatment_4", 3))
rownames(mymat) <- paste("gene", 1:dim(mymat)[1], sep="_")

mydf <- data.frame(row.names = paste("gene", 1:dim(mymat)[1], sep="_"), category = c(rep("CATEGORY_1", 10), rep("CATEGORY_2", 10), rep("CATEGORY_3", 10), rep("CATEGORY_4", 10), rep("CATEGORY_5", 10)))

# add row annotations
pheatmap(mymat, cluster_cols = F, cluster_rows = F, annotation_row = mydf)

# Add gaps
pheatmap(mymat, cluster_cols = F, cluster_rows = F, annotation_row = mydf, gaps_row = c(10, 20, 30, 40))

# Save to file with dimensions that keep both row and column names readable
pheatmap(mymat, cluster_cols = F, cluster_rows = F, annotation_row = mydf, gaps_row = c(10, 20, 30, 40), cellheight = 10, cellwidth = 20, file = "TEST.png")