I am using edgeR and ComplexHeatmap trying to plot a Heatmap with a few ATAC-seq datasets. But I came across an issue that I can't solve. So I will really appreciate if you can give me some suggestions.
When I used log transformed CPM value to plot the Heatmap, the clustering is not very clear. The Heatmap is either all in blue or all in red.
When I used "mat_scaled = t(scale(t(data)))" to scale my data before plotting, some information can't be shown in the Heatmap. Like I expected there should be values that are the same in all the samples, which should be shown in the same color across the samples. But unfortunately, after scaling, the similar values scaled to larger differences, which show different color in the Heatmap.
sample1 sample2. sample3 chr4_185974589_185974741 1.483681 1.472528 1.4296474 after scaling sample1 sample2. sample3 chr4_185974589_185974741 0.761687321 0.37073755 -1.132424873