Introduction Clustergrammer_Widget2 0.6.2

import numpy as np
import pandas as pd
import clustergrammer_widget2
from clustergrammer import *
net = Network()

net.load_file('rc_two_cats.txt')
net.cluster()
df = net.export_df()

# df.sum(axis=1)

net.load_df(df)
net.cluster()
net_json = net.export_viz_to_widget()

Visualize Example Gene Expression Toy Dataset

w = clustergrammer_widget2.ExampleWidget(network=net_json)
w

w = clustergrammer_widget2.ExampleWidget(network=net_json)
w

Visualize Random Matrix

# generate random matrix
num_rows = 1000
num_cols = 1000
np.random.seed(seed=100)
mat = np.random.rand(num_rows, num_cols)

# make row and col labels
rows = range(num_rows)
cols = range(num_cols)
rows = [str(i) for i in rows]
cols = [str(i) for i in cols]

# make dataframe 
df = pd.DataFrame(data=mat, columns=cols, index=rows)
print(df.shape)

(1000, 1000)

df.head()

	0	1	2	3	4	5	6	7	8	9	...	990	991	992	993	994	995	996	997	998	999
0	0.543405	0.278369	0.424518	0.844776	0.004719	0.121569	0.670749	0.825853	0.136707	0.575093	...	0.616522	0.947579	0.906472	0.965094	0.337621	0.656403	0.291456	0.150869	0.036932	0.597964
1	0.027732	0.382237	0.953251	0.222199	0.305126	0.819320	0.578470	0.027617	0.954388	0.312139	...	0.630891	0.478955	0.140795	0.329110	0.775616	0.633031	0.105247	0.980898	0.364798	0.778565
2	0.259444	0.023003	0.654407	0.969216	0.698952	0.032054	0.003295	0.122310	0.729892	0.743647	...	0.243378	0.935069	0.458539	0.943485	0.252805	0.205672	0.300088	0.352887	0.602199	0.478208
3	0.076735	0.568912	0.400118	0.308898	0.928405	0.234978	0.901869	0.843908	0.627951	0.858074	...	0.068109	0.494339	0.130206	0.538030	0.574568	0.078321	0.847301	0.793289	0.348319	0.966167
4	0.769620	0.043597	0.191514	0.121186	0.760843	0.623838	0.462855	0.728147	0.939783	0.267626	...	0.645082	0.220585	0.017549	0.155266	0.977466	0.237092	0.768674	0.650803	0.861580	0.108839

5 rows × 1000 columns

net.load_df(df)
net.cluster()
net_json = net.export_viz_to_widget()
w = clustergrammer_widget2.ExampleWidget(network=net_json)
w

import ipywidgets 

ipywidgets.__version__

'7.4.1'