shows the expression of genes in specific cell types in Heatmap
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Entering edit mode
3 months ago
Maria17 • 0

Hi All,

I'm working on single-cell RNA seq data with the Seurat package. I want to check the expression of some genes in some of the cell types with a heat map. currently, this code shows all of the cell types :

dittoHeatmap(Seurat.integrated, genes,
annot.by = c("PatientID", "CellType"))


how can I show the expression of genes just in some of my cell types in heatmap?

Any recommendations or solutions would be appreciated.

Thanks

Maria

dittoseq RNA-seq Seurat • 325 views
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Entering edit mode
3 months ago
Wocher33 • 0

Hi Maria,

you can subset your cells and then plot

seurat.subset <- subset(seurat.integrated, idents = "clusterofinterest")
dittoHeatmap(seurat.subset ,genes,
annot.by = c("PatientID", "CellType"))


Is that what you are looking for?

Cheers

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Entering edit mode

thank you. when subset by cell type name it greps cell type(T-cells) in all clusters but I have 5 clusters which I assigned to T cell. I want to extract these five clusters and check the gene expression.

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Entering edit mode

You can also subset by multiple clusters by combining their names as characters to a vector, eg.:

seurat.subset <- subset(seurat.integrated, idents = c("cluster1", "cluster2", "cluster3",...))