Where is the 'GEM' information used for plotting dot plots and heatmaps stored?

[changqinglu]

Dear Author,

I encountered an issue while creating dot plots and heatmaps using your example data burkhardt21. I am using the module matrix information located in adata.obsm['X_gem'], but the results differ from those in your paper. Could you please let me know where the GEM module information used for plotting dot plots and heatmaps is stored? Thank you very much for your assistance! My code is as follows:

marker = ['GEM-1', 'GEM-2', 'GEM-3', 'GEM-4', 'GEM-5', 'GEM-6', 'GEM-7', 'GEM-8', 'GEM-9', 'GEM-10']
gem_df = pd.DataFrame(adata.obsm['X_gem'], columns=['GEM-1', 'GEM-2', 'GEM-3', 'GEM-4', 'GEM-5', 'GEM-6', 'GEM-7', 'GEM-8', 'GEM-9', 'GEM-10'])
gem_df.index = adata.obs.index
adata.obs = adata.obs.join(gem_df)

sc.pl.dotplot(adata, var_names=marker, groupby='Condition', save="GEM_Condition.pdf")
sc.pl.heatmap(adata, var_names=marker, groupby='Condition', cmap='Reds', vmax=0.10, vmin=0, save="heatmap.pdf")

sc.pl.dotplot(adata, var_names=marker, groupby='leiden', save="GEM_leiden.pdf")
sc.pl.heatmap(adata, var_names=marker, groupby='leiden', cmap='Reds', vmax=0.10, vmin=0, save="leiden_heatmap.pdf")

[axelalmet]

Dear changqingliu,

I checked this myself and found a similar example between the paper and the example dataset I provided. Whereas when I looked at my own results, I got what was in the paper. I think the discrepancy comes down to how I've implemented the GEM construction method from pyLIGER, and I'm trying to figure out where the differences are.
I'll get back to you ASAP on this.

[lalalkjh]

Dear AxelAlmet,

Greetings!

I have encountered an issue while exploring and utilizing your FlowSig project, which is identical to the problem you previously described.I am curious if you have managed to find a resolution or if you have any recommendations for addressing this problem. If it is not too much trouble, could you please share your insights or suggestions? Your experience or advice would be immensely helpful in resolving my current predicament.

I look forward to your response and appreciate your willingness to assist community members amidst your busy schedule.

Best regards @axelalmet

[oyxf]

Dear AlexAlmet ,

When I use the X_gem matrix to create dotplot and heatmap, the resulting images differ from those in the article as above disscusion. Could you help me understand why this is happening and how I can adjust the parameter?

Best regard