提取heatmap聚类后行列名称

在画heatmap的时候，往往由于某种数据分析需要，需要获得聚类后的heatmap的col和row的顺序。这里展示如何从pheatmap的聚类结果中提取我们需要的信息。

这里通过产生随机数据来演示。

data <- replicate(20, rnorm(50))
rownames(data) <- paste("Gene", c(1:nrow(data)))
colnames(data) <- paste("Sample", c(1:ncol(data)))

out <- pheatmap(data, 
show_rownames=T, cluster_cols=T, cluster_rows=T, scale="row",
cex=1, clustering_distance_rows="euclidean", cex=1,
clustering_distance_cols="euclidean", clustering_method="complete", border_color=FALSE)

#Re-order original data (genes) to match ordering in heatmap (top-to-bottom)
rownames(data[out$tree_row[["order"]],])
[1] "Gene 2" "Gene 12" "Gene 9" "Gene 33" "Gene 29" "Gene 43" "Gene 24"
[8] "Gene 44" "Gene 3" "Gene 21" "Gene 46" "Gene 26" "Gene 20" "Gene 45"
[15] "Gene 18" "Gene 38" "Gene 22" "Gene 1" "Gene 17" "Gene 7" "Gene 6" 
[22] "Gene 41" "Gene 30" "Gene 31" "Gene 13" "Gene 16" "Gene 11" "Gene 50"
[29] "Gene 34" "Gene 37" "Gene 15" "Gene 25" "Gene 27" "Gene 39" "Gene 19"
[36] "Gene 35" "Gene 4" "Gene 49" "Gene 10" "Gene 28" "Gene 8" "Gene 14"
[43] "Gene 32" "Gene 42" "Gene 36" "Gene 48" "Gene 23" "Gene 47" "Gene 5" 
[50] "Gene 40"

#Re-order original data (samples) to match ordering in heatmap (left-to-right)
colnames(data[,out$tree_col[["order"]]])
[1] "Sample 3" "Sample 6" "Sample 1" "Sample 17" "Sample 8" "Sample 10"
[7] "Sample 15" "Sample 4" "Sample 18" "Sample 2" "Sample 11" "Sample 9" 
[13] "Sample 13" "Sample 12" "Sample 7" "Sample 19" "Sample 14" "Sample 16"
[19] "Sample 5" "Sample 20"

将排序后，行的名称存入文件

rowdata = rownames(data[out$tree_row[["order"]],])
write.table(rowdata,file='rowdata.txt', row.names=F, col.names = F, quote=F)

同理，将排序的列的名称存入文件

coldata = rownames(data[out$tree_col[["order"]],])
write.table(coldata,file='coldata', row.names=F, col.names = F, quote=F)

关于write.table的使用说明：

Write.table()函数的用法read.table()非常相似，只不过它把数据框写入文件而不是从文件中读取。参数和选项：

write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ",eol = "\n", na = "NA", dec = ".", row.names = TRUE,col.names = TRUE, qmethod = c("escape", "double"))

函数Write.table()的选项值及说明