Notebook for Over Representation Analysis Visualisation for SiRCle¶

N13_SiRCle_ORA_vis

Visualising the ORA data as Emapplots¶

Note you should be running at least python 3.8

In [1]:

from scircm import plot_cluster_ORA
import os

base_dir = '../data/'
data_dir = f'{base_dir}sircle/F3_regulatory_clustering/ORA_results/'
output_dir = f'{base_dir}sircle/F3_regulatory_clustering/ORA_results/'
fig_dir = '../figures/'
supp_dir = f'{base_dir}raw_downloads/supps/'
gene_name = 'hgnc_symbol'
save_fig = False
test_title = 'all_patients_ccRCC'

files = os.listdir(data_dir)
cluster_files = [c for c in files if 'ClusterGoSummary' in c]

for c in cluster_files:
    if '.svg' not in c:
        plot_cluster_ORA(f'{data_dir}{c}', figsize=(5,5))