Not getting cluster names in the dataframe after pathway expression

[jjyotikataria]

I ran the following commands after taking a clustered Seurat object.

gsva_result <- analyse_sc_clusters(pbmc, verbose = TRUE)

pathway_expression <- pathways(gsva_result)

colnames(pathway_expression) <- gsub("\.Seurat", "", colnames(pathway_expression))

In the example, the heatmap shows Cluster1 and Cluster 2 etc, in my plot it shows X0 and X1 for the two clusters. Could you please help me with it? @nturaga @hawrobin @teslajoy @jweiser @SolomonShorser-OICR

[jgriss]

Hi @jjyotikataria,

Thanks for your interest in ReactomeGSA!

The resulting names depend on your cluster names or rather the primary identifier used. For Seurat, this is done using the Idents function.

In the example, the dataset contained "Cluster 1" ... as the main Ident.

Once you adapt yours to match your cluster assignments, it should work.

Kind regards,
Johannes

Btw @nturaga this is the best place to get support for ReactomeGSA