【pheatmap热图scale报错】Error in hclust(d, method = method)：NA/NaN/Inf in foreign function call (arg 11)

初始数据类似如下：

image.png

填充下缺失值

data[data==0] <- NA
data[is.na(data)] <- min(data,na.rm = T)*0.01
pheatmap(log10(data))

pheatmap(data,scale = "row")

直接取log绘制不报错，但做scale时报错：

Error in hclust(d, method = method) : 
  NA/NaN/Inf in foreign function call (arg 11)

原因是数据中有标准差sd为0的行，做归一化时报错。pheatmap中做归一化采用的是scale方法：

image.png

因此如果要做scale，需要将这样的行去掉：

test <- data[apply(data, 1, function(x) sd(x)!=0),]
pheatmap(test,scale = "row")

Ref:
https://stackoverflow.com/questions/30350438/pheatmap-scale-row-giving-error-in-hclustd-method-method-na-nan-inf-in
https://zhuanlan.zhihu.com/p/30518877