Seurat: How to make heatmap of Log transformed expression levels
0
0
Entering edit mode
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
ADD COMMENT

Login before adding your answer.

Traffic: 1926 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6