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ZJUFanLab / scCATCH

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
https://www.sciencedirect.com/science/article/pii/S2589004220300663
GNU General Public License v3.0
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Creating UMAP and PCA Plots after Cluster Annotation and Marker Identification #37

Closed phoebe460 closed 2 years ago

phoebe460 commented 3 years ago

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 commented 2 years ago

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