Seurat: How to extract gene matrix from seurat object that have been used in generating tSNE clusters?

[bishwaG]

Hi,
I would like extract gene matrix that has been used for tSNE cluster generation. I would like to use the matrix for clonal evolution analysis.

I have used CCA worflow.

obj <- RunTSNE(object = obj,
                reduction.use = "cca.aligned",
                dims.use = 1:10,
                do.fast = TRUE)

obk <- FindClusters(object = obj,
                reduction.type = "cca.aligned",
                dims.use = 1:10,
                save.SNN = TRUE,
                force.recalc=TRUE,
                resolution=0.7)

[leonfodoulian]

Hi,

In your case, CCA cell embeddings are used for graph-based clustering and t-SNE embedding. The following code should return the first 10 CCA dimensions (i.e. those also used by Seurat when running the codes you reference):

cca.data <- GetCellEmbeddings(object = obj, reduction.type = "cca.aligned")[,1:10]

Best,
Leon