Hi,

After running T-SNE plot on dataset, I tried to extract a specific cell type then do reclustering. But I found that the some of the cell identity IDs are skipped in the reclustered T-SNE plot (0,2,3,4,6... instead of 0,1,2,3,4,5,6):

Here is my code:

DefaultAssay(combined.all) <- "integrated"

# subset Seurat to only Epithelial cells
subset.Epithelial <- subset(x = combined.all, idents = "Epithelial cells")
# run tsNE
subset.Epithelial <- RunTSNE(object = subset.Epithelial)
# run umap
subset.Epithelial <- RunUMAP(subset.Epithelial, dims = 1:20) # reduction = "pca"

# T-sne plot
Epithelial.clusters.tsne <- DimPlot(subset.Epithelial, reduction = "tsne",group.by = "seurat_clusters",label = TRUE)

I cannot figure this out nor find help from other website resources. Could anybody provide some help on how to interpret this?

Thanks so much!