pycrosstalker.tools.generate_report.analise_LR

pycrosstalker.tools.generate_report.analise_LR(input, genes=None, tf_genes=None, out_path=None, sep=',', threshold=0, colors=None, out_file=None, output_fmt='html_document', sel_columns=['source', 'target', 'gene_A', 'gene_B', 'type_gene_A', 'type_gene_B', 'MeanLR'], comparison=None, filtered_net=False, filename=None, save=True)

Core engine to generate report. Here we perform all the computation related to pyCrossTalkeR

Parameters

input :

Named vector with the lrpaths of each output or an AnnData object

genes :

list of genes to be considered in the sankey plots

out_path :

output directory path

sep :

character used on csv

threshold :

percentage of edges to be pruned

colors :

celltypes colorscheme

out_file :

output file names

output_fmt :

rmarkdown render output format parameter

sel_columns :

columns from data

filename :

filename prefix for output files (to be provided if not already present in AnnData object)

save:

Indicates if analysis file is saved or not

Returns

Rmarkdown report all objects from each step