This notebook displays interactive heatmaps of single-cell gene expression data from atherosclerotic plaque samples from a cohort of six patients.
from clustergrammer2 import net
import helper_functions as hf
df = {}
>> clustergrammer2 backend version 0.5.1
net.load_file('../data/scRNA-seq_cohort_cd4_t_cells.txt')
df['gex'] = net.export_df()
df['gex'].shape
(100, 1200)
cat_color = net.load_json_to_dict('../data/category_colors.json')
net.set_cat_colors(cat_color, axis='col', cat_index=1, cat_title='Sample')
net.set_cat_colors(cat_color, axis='col', cat_index=2, cat_title='Symptomatic')
net.set_cat_colors(cat_color, axis='col', cat_index=3, cat_title='Cell Type')
net.set_cat_colors(cat_color, axis='col', cat_index=4, cat_title='Broad CT')
net.load_df(df['gex'])
net.widget()
ExampleWidget(network='{"row_nodes": [{"name": "MALAT1", "ini": 100, "clust": 0, "rank": 14, "rankvar": 10, "g…