ComplexHeatmap: setting column_order changes plotted values
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Entering edit mode
vanbelj ▴ 10
@vanbelj-21216
Last seen 7 months ago

I'm using ComplexHeatmap to plot z-scaled data. I want to set the order of my samples (columns), which can be done by setting column_order=. However, when I use this function, the z-score values that are plotted change - it looks like the average value for the samples within a group are now plotted.

Here's a simplified example using values from 5 genes. Values for my R variables are in code chunks at the bottom.

library(DESeq2)
library(ComplexHeatmap)
library(circlize)

rlogTop25 <- (assay(rld)[sigTop25,]
z.TopLFC <- t(scale(t(rlogTop25), center=TRUE, scale=TRUE))

#Correctly Plots
Heatmap(z.TopLFC,
        col = colorRamp2(c(-3, 0, 3), c('dodgerblue', 'black', 'yellow')),
        heatmap_legend_param = list (
          title = "Z-score")
)

Correct Values Plotted

#Plots averaged(?) Z-values for group of samples
Heatmap(z.TopLFC,
        col = colorRamp2(c(-3, 0, 3), c('dodgerblue', 'black', 'yellow')),
        column_order=sort(colnames(z.TopLFC)),
        heatmap_legend_param = list (
          title = "Z-score")
)

Incorrect Values Plotted

> rlogTop25
          013_Control 013_Salt 013_Control 013_Salt 013_Control 013_Salt
YFL014W      6.347657 8.132517    6.462191 7.591956    6.360166 7.637381
YAR009C     10.166573 8.480758    9.699538 7.838010   10.682334 8.217700
YDL204W      7.560660 9.085627    7.693605 9.150839    7.633052 8.736366
YHR032C-A    5.822386 6.743593    6.025686 6.639762    5.880813 6.519343
YOL103W-B    8.929396 8.151790    9.847492 8.064004    9.552077 8.415369
> z.TopLFC
          013_Control   013_Salt 013_Control   013_Salt 013_Control   013_Salt
YFL014W    -0.9385917  1.3222492  -0.7935150  0.6375331  -0.9227476  0.6950720
YAR009C     0.8505378 -0.6040332   0.4475662 -1.1586147   1.2955512 -0.8310072
YDL204W    -0.9856466  1.0201568  -0.8107826  1.1059313  -0.8904295  0.5607705
YHR032C-A  -1.1002669  1.1544011  -0.6026881  0.9002739  -0.9572662  0.6055462
YOL103W-B   0.1376152 -0.9042738   1.3677420 -1.0218953   0.9719247 -0.5511128
attr(,"scaled:center")
  YFL014W   YAR009C   YDL204W YHR032C-A YOL103W-B 
 7.088644  9.180819  8.310025  6.271931  8.826688 
attr(,"scaled:scale")
  YFL014W   YAR009C   YDL204W YHR032C-A YOL103W-B 
0.7894670 1.1589778 0.7602771 0.4085777 0.7463425
> sort(colnames(z.TopLFC))
[1] "013_Control" "013_Control" "013_Control" "013_Salt"    "013_Salt"    "013_Salt"
ComplexHeatmap • 168 views
ADD COMMENT
0
Entering edit mode
vanbelj ▴ 10
@vanbelj-21216
Last seen 7 months ago

The reason behind the issue has to do with the column names being the same and using the sort() function. The problem can be solved in one of two ways:

1) Continue using sort() with unique samples names (e.g. Control1, Control2, Control3 ...)
-or-
2) Use order() instead of sort()

Heatmap(z.TopLFC,
        col = colorRamp2(c(-3, 0, 3), c('dodgerblue', 'black', 'yellow')),
        column_order=order(colnames(z.TopLFC)),
        heatmap_legend_param = list (
          title = "Z-score")
)
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