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authorFrederick Muriuki Muriithi2021-09-15 11:19:56 +0300
committerFrederick Muriuki Muriithi2021-09-15 11:19:56 +0300
commite3e18950cfcdec918429dcbb5d5ed2e9616b7a20 (patch)
tree52fad9c47ae0ef34739024708d1cd7cdb0e29f6d /gn3/heatmaps
parentf17b489c8eb94050b81b1a59fb43954d036f7c38 (diff)
downloadgenenetwork3-e3e18950cfcdec918429dcbb5d5ed2e9616b7a20.tar.gz
Reorganise modules
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * The heatmap generation does not fall cleanly within the computations or db modules. This commit moves it to the higher level gn3 module.
Diffstat (limited to 'gn3/heatmaps')
-rw-r--r--gn3/heatmaps/heatmaps.py67
1 files changed, 0 insertions, 67 deletions
diff --git a/gn3/heatmaps/heatmaps.py b/gn3/heatmaps/heatmaps.py
deleted file mode 100644
index 88f546d..0000000
--- a/gn3/heatmaps/heatmaps.py
+++ /dev/null
@@ -1,67 +0,0 @@
-import random
-import plotly.express as px
-
-#### Remove these ####
-
-heatmap_dir = "heatmap_images"
-
-def generate_random_data(data_stop: float = 2, width: int = 10, height: int = 30):
- """
- This is mostly a utility function to be used to generate random data, useful
- for development of the heatmap generation code, without access to the actual
- database data.
- """
- return [[random.uniform(0,data_stop) for i in range(0, width)]
- for j in range(0, height)]
-
-def generate_random_data2(data_stop: float = 2, width: int = 10, height: int = 30):
- """
- This is mostly a utility function to be used to generate random data, useful
- for development of the heatmap generation code, without access to the actual
- database data.
- """
- return [
- [{
- "value": item,
- "category": random.choice(["C57BL/6J +", "DBA/2J +"])}
- for item in axis]
- for axis in generate_random_data(data_stop, width, height)]
-
-def heatmap_x_axis_names():
- return [
- "UCLA_BXDBXH_CARTILAGE_V2::ILM103710672",
- "UCLA_BXDBXH_CARTILAGE_V2::ILM2260338",
- "UCLA_BXDBXH_CARTILAGE_V2::ILM3140576",
- "UCLA_BXDBXH_CARTILAGE_V2::ILM5670577",
- "UCLA_BXDBXH_CARTILAGE_V2::ILM2070121",
- "UCLA_BXDBXH_CARTILAGE_V2::ILM103990541",
- "UCLA_BXDBXH_CARTILAGE_V2::ILM1190722",
- "UCLA_BXDBXH_CARTILAGE_V2::ILM6590722",
- "UCLA_BXDBXH_CARTILAGE_V2::ILM4200064",
- "UCLA_BXDBXH_CARTILAGE_V2::ILM3140463"]
-#### END: Remove these ####
-
-# 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