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authorMuriithi Frederick Muriuki2021-08-12 17:21:44 +0300
committerArun Isaac2021-08-18 08:47:34 +0000
commit3d1595d1fcc5085621ef8ce41a007d283595c7c6 (patch)
tree2580896397b6a9bb203a7be3b9ee7c931605b5b7
parent70ed53f03f3d74877d5bc71e49e3a1e65af8b15f (diff)
downloadgenenetwork3-3d1595d1fcc5085621ef8ce41a007d283595c7c6.tar.gz
Initialise heatmap generation module
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/heatmaps/heatmaps.py: Initialise the module with some code to be used to test out plotly features on the command-line. * guix.scm: Add `python-plotly` and `python-pandas` as dependencies.
-rw-r--r--gn3/heatmaps/heatmaps.py54
-rw-r--r--guix.scm5
2 files changed, 58 insertions, 1 deletions
diff --git a/gn3/heatmaps/heatmaps.py b/gn3/heatmaps/heatmaps.py
new file mode 100644
index 0000000..3bf7917
--- /dev/null
+++ b/gn3/heatmaps/heatmaps.py
@@ -0,0 +1,54 @@
+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 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():
+ rows = 20
+ data = generate_random_data(height=rows)
+ y = (["%s"%x for x in range(1, rows+1)][:-1] + ["X"]) #replace last item with x for now
+ fig = px.imshow(
+ data,
+ x=heatmap_x_axis_names(),
+ y=y,
+ 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
diff --git a/guix.scm b/guix.scm
index f94fe1a..729d089 100644
--- a/guix.scm
+++ b/guix.scm
@@ -38,6 +38,7 @@
(gn packages python)
(gnu packages base)
(gnu packages check)
+ (gnu packages graph)
(gnu packages cran)
(gnu packages databases)
(gnu packages statistics)
@@ -101,7 +102,9 @@
,python-sqlalchemy-stubs)
("r-optparse" ,r-optparse)
("r-qtl" ,r-qtl)
- ("r-stringi" ,r-stringi)))
+ ("r-stringi" ,r-stringi)
+ ("python-plotly" ,python-plotly)
+ ("python-pandas" ,python-pandas)))
(build-system python-build-system)
(home-page "https://github.com/genenetwork/genenetwork3")
(synopsis "GeneNetwork3 API for data science and machine learning.")