I’m working on a single cell project and have done your typical pre-processing by log-normalizing and scaling the data. I want to generate heatmaps that depict the z-score of each differentially expressed across all cells. I performed differential gene expression analysis using the
rank_genes_groups() function with the Wilcoxon test. After looking through the documentation, I’m quite confused on a few things. First, the documentation states that the “score” generated from the Wilcoxon test is the z-score, and the docs also state that plotting the DGE using the
rank_genes_groups_heatmap() produces a heatmap of the “ranking of genes using a heatmap”. My question is: what exactly is being plotted when calling the
rank_genes_groups_heatmap() function? Is it the log-normalized and scaled expression stored in adata.X? or is it the z-score produced by the Wilcoxon test? The heatmap looks like this:
I also tried another approach to producing the z-score heatmap. in the alternative approach, I simply calculated the z-score of the log-normalized counts that I stored in an anndata layer, called “counts-lognorm”, and then saved the z-score calculation in another layer, called “z-score”. When trying to make the heatmap using the
heatmap() and passing the “z-score” layer to the layers parameter, my heatmap is completely different than the heatmap generated above and is almost all dark blue.
Can the community please help me generate a heatmap depicting z-scores?
Thanks in advanced