I have a strange error that I cannot seem to fix myself. I calculate irGSEA.score on a seurat object with 4 clusters. My problem is that when I change identity of the seurat object to labels from a metadata column, where two clusters have the same label, I no longer see the direction in the heatmap.
I use the following code:
I have a strange error that I cannot seem to fix myself. I calculate irGSEA.score on a seurat object with 4 clusters. My problem is that when I change identity of the seurat object to labels from a metadata column, where two clusters have the same label, I no longer see the direction in the heatmap. I use the following code:
`seu_obj <- irGSEA.score(object = seu_obj, assay = "RNA", slot = "data", seeds = 123, ncores = 1, min.cells = 3, min.feature = 0, custom = T, geneset = metabolism.go, geneid = "symbol", method = c("AUCell", "UCell", "singscore", "ssgsea"), aucell.MaxRank = NULL, ucell.MaxRank = NULL, kcdf = 'Gaussian')
result.dge <- irGSEA.integrate(object = seu_obj, group.by = NULL, metadata = NULL, col.name = NULL, method = c("AUCell","UCell", "singscore", "ssgsea"))
irGSEA.heatmap.plot <- irGSEA.heatmap(object = result.dge, method = "UCell", top = 50, show.geneset = NULL, cluster_rows = FALSE) irGSEA.heatmap.plot`
This is with 4 clusters:
This is with 3 groups:
The only difference is whether I use
Idents()to change identity.Does anyone have an idea to why this occurs?