pheatmap :提取行z得分值

Question

我对pheatmap中的行缩放有些困惑。这是我的数据框

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

我需要在pheatmap生成带有行z得分的图形之后提取数据帧的这些值

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 = "row",         
         cluster_cols=FALSE,    
         cluster_rows = FALSE,
         treeheight_row=0,      
         show_rownames=FALSE,   
         main = "test.txt",
         color = my_palette,
         breaks = my_colors)

我怎样才能得到一个新的矩阵，pheatmap使用它来制作热图？

Answer 1

scale_rows = function(x){
    m = apply(x, 1, mean, na.rm = T)
    s = apply(x, 1, sd, na.rm = T)
    return((x - m) / s)
}

zscores <- scale_rows(matrix)

https://github.com/raivokolde/pheatmap/blob/44a44f7e640c73867f40261691c16dfa4da34fa8/R/pheatmap.r