Creating UMAP and PCA Plots after Cluster Annotation and Marker Identification

[phoebe460]

Hello scCATCH developers,

First off, thanks for creating this great tool. I am using it now for my single-cell analysis, and it's been working great so far.

So I've done the following for my analysis:

clu_markers <- findmarkergenes(cells_human_tc, species = 'Human', cluster = 'All', match_CellMatch = FALSE, cancer = NULL, tissue = c('Brain','Dorsolateral prefrontal cortex'), cell_min_pct = 0.1, #as recommended by Issues Github page logfc = 0.1, #as recommended by Issues Github page pvalue = 0.05)

clu_ann <- scCATCH(clu_markers_v2, species = 'Human', tissue = 'Brain')

Since I have the markers and annotated clusters identified, is there a way to get UMAP and PCA plots from this? If so, is there a way to visualize my annotated clusters code wise? If you can help out with this, then that would be greatly appreciated.

Thanks,
Phoebe

[multitalk]

I suggest to use Seurat to get UMAP and PCA plots.