How to define "atac_anndata" in the toturial ??

[bitcometz]

hello, thanks for this great tool !!!
I try to learn this tool by the toturial.
However, I cannot run this step, since the var "atac_anndata" only appear once:

from pycisTopic.label_transfer import *
label_dict = label_transfer(rna_anndata,
                  atac_anndata,
                  labels_to_transfer = ['Seurat_cell_type'],
                  variable_genes = True,
                  methods = ['ingest', 'harmony', 'bbknn', 'scanorama', 'cca'],
                  return_label_weights = False,
                  _temp_dir= tmpDir + 'ray_spill')

Could you please tell how to define it ?

Thanks !!!!

[SeppeDeWinter]

Hi @bitcometz

I guess we missed it in the tutorial.

You can generate it like this (following this tutorial https://pycistopic.readthedocs.io/en/latest/Single_sample_workflow-RTD.html)

# Prepare ATAC
import pickle
infile = open(outDir + 'DAGs/Gene_activity.pkl', 'rb') #Here I am using pycisTopic gene activity matrix, but could be any :)
gene_act = pickle.load(infile)
infile.close()
atac_anndata = anndata.AnnData(X=gene_act)