wdg118

> Yeah. or you could install gseapy from source. > > and rust too. > > ```shell > curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh > ``` I tried...

Hi @gaddamshreya, Thank you for your reply. Here is a screenshot of the error for `tg.plot_cell_annotation_sc`  It seems this function only works for Visium data. In relation to Fig.2,...

Hi Shreya, Thanks for this. I'm currently in my classes this week and I'm reinstalling all of my conda environments and I will run it again and send you the...

Hi Isaïas, Thanks for this, I will try it. Shreya has just replied and I need to show her the output of the .uns of my spatial data, but nonetheless...

Hi again Shreya, I just looked at the documentation since I remembered that tg.plot_cell_annotation(ad_map,adata_st,annotation='subclass_label',nrows=5, ncols=5,robust=True, perc=0.02) and tg.plot_genes(genes, adata_measured=adata_st, that the arguments for the function do not seem to match...

Hi Shreya, Oh right. I remember trying these previously and they also did not work. I will try them again once I fix my conda environment issues and get back...

Hi Shreya, Here is the output of adata_st.uns.get("spatial", {}).keys(): [image: image.png] Here is the error message I get when I run tg.plot_cell_annotation(ad_ map,adata_st,annotation='predicted.subclass_Allen',nrows=5, ncols=5,robust=True, perc=0.02) INFO:root:spatial prediction dataframe is saved...

Hi @gaddamshreya, Sorry, I replied via email and it didn't show here. Here is the output from adata_st.uns.get("spatial", {}).keys()  My Anndata has 'min_x', 'max_x', 'min_y', and 'max_y', so I...

Hi @johannesostner, What metric do we use for pairwise comparisons ? Final Parameter ? Thanks!

Hi @johannesostner , Thanks for clarifying this. I appreciate it! Also I'm assuming the model accounts and corrects for multiple comparisons? I believe this can be inferred from the fact...