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JCVenterInstitute / NSForest

A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA sequencing
MIT License
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Question about the ns.pl.dotplot dendrogram variable #19

Open Charithwij opened 3 months ago

Charithwij commented 3 months ago

While following through the readthedocs tutorial, I have some confusion about the dotplot function. ns.pl.dotplot(adata, markers_dict, cluster_header, dendrogram = dendrogram, save = True, output_folder = output_folder, outputfilename_suffix = outputfilename_prefix)

Setting dendrogram=True functionally makes no changes to the order of the data, while also adding a dendrogram on the right side of the dotplot. Is there supposed to be a difference between the two options besides adding the dendrogram?

adeslatt commented 3 months ago

I just now created a pull request - when I created a notebook (did this on my mac book pro laptop) -- everything did run perfectly - only thing missing was the scanpy package - I did not start from a completely clean conda environment -- will do so if my pull request is accepted then I will add some additional documentation.