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corceslab / CHOIR

CHOIR : Clustering Hierarchy Optimization by Iterative Random forests (www.CHOIRclustering.com)
MIT License
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plotCHOIR split.by option #9

Closed Carolina-Toste closed 6 months ago

Carolina-Toste commented 6 months ago

Hi there,

Thank you so much for this package, it's really great . I've been testing it on my data and I have successfully plotted the CHOIR clusters umap plot. I wanted to try to plot these clusters split.by genotype, but that functionality seems not to be supported(unless I'm somehow made a mistake). Could you let me know if by any chance this will change in the future? I did manage to get the plot I wanted with

DimPlot(seurat, pt.size=2, split.by ="Genotype", group.by = "CHOIR_clusters_0.05", reduction ="CHOIR_P0_reduction_UMAP")
catpetersen commented 6 months ago

Hi! Glad you like the package!

This is a good catch—I've made some changes to plotCHOIR() to accommodate more of the Seurat::DimPlot parameters like split.by in a new branch: 'dev_seurat_compatibility'.

Would you try reinstalling CHOIR with this branch, and let me know if split.by works for you?

remotes::install_github("corceslab/CHOIR", ref = "dev_seurat_compatibility", repos = BiocManager::repositories(), upgrade = "never")
# To unload a package and reload
detach("package:CHOIR", unload = TRUE)
library(CHOIR)
catpetersen commented 6 months ago

Hi! I'm closing this issue for now, but please feel free to reply here if you have any additional issues and I'll reopen it.