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theislab / scCODA

A Bayesian model for compositional single-cell data analysis
BSD 3-Clause "New" or "Revised" License
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How to plot the final result? #98

Closed mainharryHR closed 4 months ago

mainharryHR commented 4 months ago

Dear team,

Thanks for the great package

I believe I have already generate all the comparisons. But when I try to plot, I only can see the one comparison, but not able to plot other comparisons. pt.pl.coda.effects_barplot(sccoda_data_control, "coda", "Cancer") plt.show()

AnnData object with n_obs × n_vars = 24 × 15 varm: 'intercept_df', 'effect_df_Cancer[T.No]', 'effect_df_Cancer[T.CRC]', "effect_df_C(Cancer, Treatment('Control'))[T.No]", "effect_df_C(Cancer, Treatment('Control'))[T.CRC]", "effect_df_C(Cancer, Treatment('No'))[T.Control]", "effect_df_C(Cancer, Treatment('No'))[T.CRC]"

Screenshot 2024-05-20 at 10 06 16

Any comments are welcome!

johannesostner commented 4 months ago

Hi @mainharryHR, this is the repository for scCODA's initial implementation. You are referring to a functionality from the reimplementation in the pertpy package (https://github.com/theislab/pertpy). Please ask your question over there!