Seurat: How to make heatmap of Log transformed expression levels
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5 months ago
pv6077 • 0

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!

seurat RNA-Seq R • 668 views

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