def dendrogram_heatmap(output_dir: str, table: pd.DataFrame,
tree: TreeNode, metadata: MetadataCategory,
ndim=10, method='clr', color_map='viridis'):
nodes = [n.name for n in tree.levelorder() if not n.is_tip()]
nlen = min(ndim, len(nodes))
numerator_color, denominator_color = '#fb9a99', '#e31a1c'
highlights = pd.DataFrame([[numerator_color, denominator_color]] * nlen,
index=nodes[:nlen])
if method == 'clr':
mat = pd.DataFrame(clr(centralize(table)),
index=table.index,
columns=table.columns)
elif method == 'log':
mat = pd.DataFrame(np.log(table),
index=table.index,
columns=table.columns)
# TODO: There are a few hard-coded constants here
# will need to have some adaptive defaults set in the future
fig = heatmap(mat, tree, metadata.to_series(), highlights, cmap=color_map,
highlight_width=0.01, figsize=(12, 8))
fig.savefig(os.path.join(output_dir, 'heatmap.svg'))
fig.savefig(os.path.join(output_dir, 'heatmap.pdf'))
css = r"""
.square {
float: left;
width: 100px;
height: 20px;
margin: 5px;
border: 1px solid rgba(0, 0, 0, .2);
}
.numerator {
background: %s;
}
.denominator {
background: %s;
}
""" % (numerator_color, denominator_color)
index_fp = os.path.join(output_dir, 'index.html')
with open(index_fp, 'w') as index_f:
index_f.write('<html><body>\n')
index_f.write('<h1>Dendrogram heatmap</h1>\n')
index_f.write('<img src="heatmap.svg" alt="heatmap">')
index_f.write('<a href="heatmap.pdf">')
index_f.write('Download as PDF</a><br>\n')
index_f.write('<style>%s</style>' % css)
index_f.write('<div class="square numerator">'
'Numerator<br/></div>')
index_f.write('<div class="square denominator">'
'Denominator<br/></div>')
index_f.write('</body></html>\n')
def dendrogram_heatmap(output_dir: str,
table: pd.DataFrame,
tree: TreeNode,
metadata: MetadataCategory,
ndim=10,
method='clr',
color_map='viridis'):
nodes = [n.name for n in tree.levelorder()]
nlen = min(ndim, len(nodes))
highlights = pd.DataFrame([['#00FF00', '#FF0000']] * nlen,
index=nodes[:nlen])
if method == 'clr':
mat = pd.DataFrame(clr(centralize(table)),
index=table.index,
columns=table.columns)
elif method == 'log':
mat = pd.DataFrame(np.log(table),
index=table.index,
columns=table.columns)
# TODO: There are a few hard-coded constants here
# will need to have some adaptive defaults set in the future
fig = heatmap(mat,
tree,
metadata.to_series(),
highlights,
cmap=color_map,
highlight_width=0.01,
figsize=(12, 8))
fig.savefig(os.path.join(output_dir, 'heatmap.svg'))
index_fp = os.path.join(output_dir, 'index.html')
with open(index_fp, 'w') as index_f:
index_f.write('<html><body>\n')
index_f.write('<h1>Dendrogram heatmap</h1>\n')
index_f.write('<img src="heatmap.svg" alt="heatmap">')
index_f.write('</body></html>\n')