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Feature plot not applicable for RunTSNE object in seurat?

enter image description here

Dear All,

I visualized my cluster using tsne object (image attached) and would like to run FeaturePlot to examine the expression of particular gene, but it did not work for tsne object.

I could only do it with UMAP. Any suggestion to visualize particular gene in all clusters using tsne object.

Thanks,

library(harmony)
set.seed(15874)
Tcell.cluster_TSNE<-  RunHarmony(Tcell.cluster, group.by.vars = "orig.ident")
Tcell.cluster_TSNE <- FindNeighbors(Tcell.cluster_TSNE, reduction= "harmony", dims = 1:30)
Tcell.cluster_TSNE <- FindClusters(Tcell.cluster_TSNE, resolution = 0.8)
Tcell.cluster_TSNE <- RunTSNE(Tcell.cluster_TSNE, reduction = "harmony", dims = 1:30)

# Feature plot
FeaturePlot(Tcell.cluster_TSNE, features = c("CD4", "CD8A", "FOXP3", "GNLY"))
harmony seurat single-cell
• 1,512 views • link
written by synat.keam • synat.keam

1 answer

You need to define reduction in your FeaturePlot function-

FeaturePlot(Tcell.cluster_TSNE, features = c("CD4", "CD8A", "FOXP3", "GNLY"), reduction = "tsne")
• 0 views • link
written by bk11 • bk11

Thank you so much senior. it worked now. much appreciated.

• 0 views • link
written by synat.keam • synat.keam

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