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enblacar / SCpubr

Generate high quality, publication ready visualizations for single cell transcriptomics data.
https://enblacar.github.io/SCpubr-book/
GNU General Public License v3.0
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REQUEST | do_DimPlot | using "split.by" I do not want to see a "combined" plot #45

Closed Elo-mars closed 11 months ago

Elo-mars commented 11 months ago

Hello,

first of, thanks SCpubr team, this tool is great, use it a lot!

Since I upgraded to version 2, when I do a dimplot with the split.by option, I have an extra plot on my file --> "combined"
is there an option to not add this plot? sorry if it's already been discussed, I cannot find my answer anywhere. 

Thanks!

Elodie

eg

SCpubr::do_DimPlot(Seurat_Final,label=FALSE, reduction = "umap", split.by = "Tissue", group.by="Cluster", pt.size=1,legend.icon.size=6, font.size=30, ncol=3)

SCpubr version:

‘2.0.1’
enblacar commented 11 months ago

Hi @Elo-mars,

Thanks a lot for using my package! And apologies for the current status of the documentation for v2, a lot of things piled up currently in my PhD that prevent me from currently investing heavy time on the package...

I do hope, still, that you are enjoying SCpubr v2!

The "Combined" plot was a necessity arising due to the way the plot is generated when using group.by + split.by. If you happen not to have at least a single cell for each of the groups you want to show in group.by, this will result in the end plot having multiple legends. Hence, the use of the "Combined" plot, to avoid exactly this scenario. This is an intended feature and will remain as is as long as I do not find a more suitable solution (I was also not super happy about it either, but was still better than having multiple legends).

However, as a side effect, this "Combined" plot also shows up when using split.by alone. This I have it noted down and should be fixed in the next update.

Hope this was helpful! Feel free to open new issues if you have any more doubts.

Best, Enrique

Elo-mars commented 11 months ago

Hi Enrique,

thanks for the quick reply!

ok, noted, we will just crop the combined umap in the manuscript then ;) didn't think of the issue you mentionned

Cheers,

Elodie

enblacar commented 11 months ago

Good luck with the revision! 🤞

enblacar commented 10 months ago

Hi @Elo-mars,

I have just committed changes that allow toggling on and off the combined view with the parameter split.by.combined. If you want to access them, you should download and install the latest commit. They will roll out in the next update.

However, the use of split.by alongside group.by will still have the combined view enforced, to avoid the problems I mentioned before.

I thought you might want to know it, in case you also had the same problems when only using split.by!

Best, Enrique