I'm new to single-cell sequencing analysis so I am sorry if this is a super simple question. I am working with a single-cell sequencing dataset and I'm trying to generate a heatmap of the average expression levels of select genes in select clusters. This is what I did:
avgexp <- AverageExpression(seurat.object, features = c("genes", "of", "interest"), return.seurat = TRUE) subset.1 <- subset(avgexp, idents = "clusters", "of", "interest")
The way I understand it , performing DoHeatmap(subset.1) plots scaled expression data, useful for telling apart "high expressing" and "low expressing" clusters for each gene. But if I want to make between-gene expression level comparisons I am thinking I would need the heatmap to plot the non-scaled log-transformed expression levels instead. I thought I could use
DoHeatmap(subset.1, slot = "data")
to do this, but according to the heatmap legend, the data is still scaled. Is there something I am missing here or not understanding?
Thank you!
