Feature plot not applicable for RunTSNE object in seurat?

Question

[synat.keam]

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"))

Answer 1

[bk11]

You need to define reduction in your FeaturePlot function-

FeaturePlot(Tcell.cluster_TSNE, features = c("CD4", "CD8A", "FOXP3", "GNLY"), reduction = "tsne")

[synat.keam]

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