Something wrong in genemodule/plot_geneemb.ipynb

[Peg-Wu]

Hello, developer!

I found an error while running the genemodule/plot_geneemb.ipynb code:

coexplist=[]
for tf in tqdm(fltTF):
    tmpsim = cosine_similarity(fltgeneembdf.loc[fltTF[0],:].values.reshape(1,-1),fltgeneembdf)
    tmpsim[tmpsim>0.9999]=0
    tmpsimdf = pd.DataFrame(tmpsim,columns=sgene,index=['simi']).T
    tmpsimdf = tmpsimdf.sort_values('simi',ascending=False)
    for idx in range(1000):
        coexplist.append([tf,tmpsimdf.index[idx],tmpsimdf.iloc[idx,0]*100])

There is a problem with the following code:

tmpsim = cosine_similarity(fltgeneembdf.loc[fltTF[0],:].values.reshape(1,-1),fltgeneembdf)

fltgeneembdf.loc[fltTF[0],:].values.reshape(1,-1) should be modified as fltgeneembdf.loc[tf,:].values.reshape(1,-1)

[WhirlFirst]

Hi,

Thank you for checking this! It seems that the rest parts of pySCENIC have done some corrections by AUCell mode to get the final results. We will take a look and fix this. Thanks