Exporting rankgenegroups to pandas dataframes

[Fougere87]

What kind of feature would you like to request?

Additional function parameters / changed functionality / changed defaults?

Please describe your wishes

Hi scanpy and thank you for your work :-) ,

I created a small function to export rank_gene_groups genes to panda Dataframes, so I'm proposing it:

Here is the code:

def get_df_of_rank_gene_groups(adata, key): 
    """Returns a dictionnary containing the differentially expressed genes in "key" in dataframes."""    
    rgg=adata.uns[key].copy()    
    if "params" in rgg :
        params=rgg.pop("params")     
    groups=list(rgg["names"].dtype.names) 
    d_return={}     
    for g in groups :
        df_g = pd.DataFrame({key:rgg.get(key)[g]for key in rgg.keys() if key not in ["pts", "pts_rest"]},                  
                            columns= rgg.keys())     
        df_g.index=df_g.pop("names") 
        
        if "pts" in rgg.keys():
            df_g.pop("pts") 
            if "pts_rest" in rgg.keys():
                df_g.pop("pts_rest")
                pts_df=pd.DataFrame({"pts":rgg.get("pts")[g],"pts_rest":rgg.get("pts_rest")[g]}, index=adata.var_names )
            else:
                pts_ref=rgg.get("pts")[rgg.get("pts").columns.difference(rgg["names"].dtype.names)]
                pts_df=pd.DataFrame({"pts":rgg.get("pts")[g], "pts_rest":pts_ref.iloc[:,0]}, index=adata.var_names )
            df_g=pd.concat([df_g,pts_df], axis=1)
        d_return[g]=df_g  
    
    if len(groups) > 1:         
        return d_return     
    else :         
        return d_return[groups[0]]

Depending on the number of groups, it returns a dictionnary, or a single dataframe, with genes names, pvalues and proportions of cells expressing.

I'm sure it needs improvments but it can really be useful to export DEGs for publication or sharing.

Best

[maltekuehl]

Hi, I'm not a maintainer of scanpy, just happened to see this. Are you aware of sc.get.rank_genes_groups_df? What additional functionality does your code add and could this be implemented as a change to the existing function?

[Fougere87]

Hi,
Thank you Malte! No I was not aware of that one in the get module ! And I believe it does everything we need as it seems to also incluse pts.
So all good !