def build_layout():
df = load_data.load_gsva_compare_cluster('hallmark')
# TODO THIS NEEDS TO BE CLEANED UP!!!!!!
cat_to_true = defaultdict(lambda: [])
for clust in df.index:
if 'PJ030' in clust:
cat_to_true['LGG'].append(clust)
elif 'PJ' in clust:
cat_to_true['GBM'].append(clust)
elif 'LX' in clust:
cat_to_true['LUAD'].append(clust)
elif 'GSE146026' in clust:
cat_to_true['OV'].append(clust)
elif 'GSE72056' in clust:
cat_to_true['SKCM'].append(clust)
elif 'GSE103322' in clust:
cat_to_true['HNSC'].append(clust)
elif 'GSE111672' in clust:
cat_to_true['PAAD'].append(clust)
cats = [{
'title': 'Cancer Type',
'cats': {k: v
for k, v in cat_to_true.items()}
}]
net = Network()
net.load_df(df)
net.add_cats('row', cats)
net.make_clust()
layout = dcc.Tab(label='Cluster Comparison',
children=[
dbc.Container(
fluid=True,
children=[
html.Link(rel='stylesheet',
href='./static/custom.css'),
dash_clustergrammer.DashClustergrammer(
id='cgram-component',
label='',
network_data=net.viz)
])
])
return layout
def prepare_heatmap(matrix_input, html_file, html_dir, tools_dir, categories, distance, linkage):
# prepare directory and html
os.mkdir(html_dir)
env = Environment(loader=FileSystemLoader(tools_dir + "/templates"))
template = env.get_template("clustergrammer.template")
overview = template.render()
with open(html_file, "w") as outf:
outf.write(overview)
json_output = html_dir + "/mult_view.json"
net = Network()
net.load_file(matrix_input)
if (categories['row']):
net.add_cats('row', categories['row'])
if (categories['col']):
net.add_cats('col', categories['col'])
net.cluster(dist_type=distance, linkage_type=linkage)
net.write_json_to_file('viz', json_output)
def get_clustergrammer_json(self, outfile):
# Create network
net = Network()
# Load file
net.load_df(self.expression_dataframe)
# Add categories
try:
net.add_cats('col', self.sample_cats)
except:
pass
try:
# calculate clustering using default parameters
net.cluster()
# save visualization JSON to file for use by front end
net.write_json_to_file('viz', outfile)
except:
os.system('touch {outfile}'.format(**locals()))
