From e9fb4e45cfc52c5d86ef534b0e7f42ba8f4c84d3 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 15 Sep 2021 12:28:56 +0300
Subject: Generate heatmaps in a single plot
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add a function to generate the heatmaps for each chromosome into a single
plot.
---
gn3/heatmaps.py | 65 ++++++++++++++++++++++++++++++++++++---------------------
1 file changed, 41 insertions(+), 24 deletions(-)
diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py
index 0c00d6c..f3d7d25 100644
--- a/gn3/heatmaps.py
+++ b/gn3/heatmaps.py
@@ -4,6 +4,7 @@ generate various kinds of heatmaps.
"""
from functools import reduce
+from gn3.settings import TMPDIR
from typing import Any, Dict, Sequence
from gn3.computations.slink import slink
from gn3.computations.qtlreaper import generate_traits_file
@@ -296,27 +297,43 @@ def process_traits_data_for_heatmap(data, trait_names, chromosome_names):
for chr_name in chromosome_names]
return hdata
-# # Grey + Blue + Red
-# def generate_heatmap():
-# cols = 20
-# y_axis = (["%s"%x for x in range(1, cols+1)][:-1] + ["X"]) #replace last item with x for now
-# x_axis = heatmap_x_axis_names()
-# data = generate_random_data(height=cols, width=len(x_axis))
-# fig = px.imshow(
-# data,
-# x=x_axis,
-# y=y_axis,
-# width=500)
-# fig.update_traces(xtype="array")
-# fig.update_traces(ytype="array")
-# # fig.update_traces(xgap=10)
-# fig.update_xaxes(
-# visible=True,
-# title_text="Traits",
-# title_font_size=16)
-# fig.update_layout(
-# coloraxis_colorscale=[
-# [0.0, '#3B3B3B'], [0.4999999999999999, '#ABABAB'],
-# [0.5, '#F5DE11'], [1.0, '#FF0D00']])
-# fig.write_html("%s/%s"%(heatmap_dir, "test_image.html"))
-# return fig
+def generate_clustered_heatmap(
+ data, image_filename_prefix, x_axis = None, x_label: str = "",
+ y_axis = None, y_label: str = "", output_dir: str = TMPDIR,
+ colorscale = [
+ [0.0, '#3B3B3B'], [0.4999999999999999, '#ABABAB'],
+ [0.5, '#F5DE11']], [1.0, '#FF0D00']):
+ """
+ Generate a dendrogram, and heatmaps for each chromosome, and put them all
+ into one plot.
+ """
+ num_cols = len(x_axis)
+ fig = make_subplots(
+ rows=1,
+ cols=num_cols,
+ shared_yaxes="rows",
+ # horizontal_spacing=(1 / (num_cols - 1)),
+ subplot_titles=x_axis
+ )
+ hms = [go.Heatmap(
+ name=chromo,
+ y = y_axis,
+ z = data_array,
+ showscale=False) for chromo, data_array in zip(x_axis, data)]
+ for col, hm in enumerate(hms):
+ fig.add_trace(hm, row=1, col=(col + 1))
+
+ fig.update_traces(
+ showlegend=False,
+ colorscale=colorscale,
+ selector={"type": "heatmap"})
+ fig.update_traces(
+ showlegend=True,
+ showscale=True,
+ selector={"name": x_axis[-1]})
+ fig.update_layout(
+ coloraxis_colorscale=colorscale
+ )
+ image_filename = "{}/{}.html".format(output_dir, image_filename_prefix)
+ fig.write_html(image_filename)
+ return image_filename, fig
--
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