r - R gplots 中的 heatmap.2 错误

Question

我在 gplots 中使用 heatmap.2 在 R 中创建热图。我的代码过去可以很好地创建热图。但最近它开始抛出错误。我不确定为什么会这样。

# Matrix to feed heatmap.2
mat = as.matrix(sort_pkmat)
# color palette for diff. colors
my_palette <- colorRampPalette(c("white","red","red4"))(n = 299)
# color breaks for range
col_breaks = c(seq(0,40,length=100),
               seq(40,60,length=100),
               seq(60,90,length=100))

path1 = paste(path,name,'.png', sep = '')
print(path1)
png(path1, 
    width = 10*300,        # 5 x 300 pixels
    height = 8*300,
    res = 300,            # 300 pixels per inch
    pointsize = 8)


heatmap.2(mat, 
          #cellnote = mat,  # same data set for cell labels
          main = "Tag_density_HeatMap", # heat map title
          xlab = "Peaks",
          ylab = "Chip_samples",
          labRow = FALSE,
          labCol = FALSE,
          cexRow = 0.7,           # Changes the size of col and row font size
          cexCol = 0.2,
          notecol="black",      # change font color of cell labels to black
          density.info="none",  # turns off density plot inside color legend
          trace="none",         # turns off trace lines inside the heat map
          margins =c(3,5),     # widens margins around plot
          col=my_palette,       # use on color palette defined earlier
          breaks=col_breaks,    # enable color transition at specified limits
          dendrogram="none",     # only draw a row dendrogram
          Colv= FALSE,           #cluster column
          Rowv = FALSE,
          #keysize = 1
)
dev.off()

现在它抛出错误:

Error in seq.default(min.raw, max.raw, by = min(diff(breaks)/4)) : 
  invalid (to - from)/by in seq(.)
> dev.off()
null device 
          1 

此代码绘制热图，但不绘制颜色键。

Answer 1

我在使用 heatmap.2 时遇到了同样的问题。这似乎是 diff(breaks) 返回的向量中有一个或多个零值的结果。当 min(diff(breaks)) 为零时，'by' 调用失败。我将断点更改为不重叠，并且能够显示颜色键。

最初我有:breaks=c(seq(0,0.033,length=25),seq(0.033,0.066,length=26),seq(0.066,0.1,length=25))

我将其更改为:breaks=c(seq(0,0.033,length=25),seq(0.0331,0.066,length=26),seq(0.0661,0.1,length=25))

它似乎已经解决了问题并允许我再次使用颜色键。