I have a Seurat object of four cancers and four controls

> colnames([email protected])
 [1] "orig.ident"       "nCount_RNA"       "nFeature_RNA"     "samples"         
 [5] "Condition"        "Gender"           "percent.mt"       "nCount_SCT"      
 [9] "nFeature_SCT"     "SCT_snn_res.0.75" "seurat_clusters"  "SCT_snn_res.0.5" 
> unique([email protected]$Condition)
[1] "control" "cancer" 

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I want to have a heat map of differentially expressed between cancers and controls like figure 3A in this paper


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Do you have any idea please how I can do that? I've looked at the integration tutorial, but can't find the heatmap in it.


1 Answer 1


See the DoHeatmap function in Seurat, which seems to be what that paper has used:


> DoHeatmap(pbmc, features = myGeneList, group.by="Condition")

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