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authorFrederick Muriuki Muriithi2021-09-22 07:53:53 +0300
committerFrederick Muriuki Muriithi2021-09-22 07:57:21 +0300
commitcd7f301688fd9780df1f842f8bd2b7602775ba1f (patch)
treecdbcf8077c532c1b5ba7bc0c934932c1a6eb58ab /gn3/heatmaps.py
parent5892ffc7488b0c9cbb4ea08fd5c5f8648e0baea8 (diff)
downloadgenenetwork3-cd7f301688fd9780df1f842f8bd2b7602775ba1f.tar.gz
Fix pylint errors
* Add missing function and module docstrings * Remove unused imports * Fix import order * Rework some code sections to fix issues * Disable some pylint errors.
Diffstat (limited to 'gn3/heatmaps.py')
-rw-r--r--gn3/heatmaps.py28
1 files changed, 16 insertions, 12 deletions
diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py
index cd93b3f..9d82fb2 100644
--- a/gn3/heatmaps.py
+++ b/gn3/heatmaps.py
@@ -3,29 +3,28 @@ This module will contain functions to be used in computation of the data used to
generate various kinds of heatmaps.
"""
+from functools import reduce
from typing import Any, Dict, Sequence
+
import numpy as np
-from functools import reduce
-from gn3.settings import TMPDIR
import plotly.graph_objects as go
import plotly.figure_factory as ff
+from plotly.subplots import make_subplots
+
+from gn3.settings import TMPDIR
from gn3.random import random_string
from gn3.computations.slink import slink
-from plotly.subplots import make_subplots
from gn3.computations.correlations2 import compute_correlation
from gn3.db.genotypes import (
- build_genotype_file, load_genotype_samples, parse_genotype_file)
+ build_genotype_file, load_genotype_samples)
from gn3.db.traits import (
- retrieve_trait_data,
- retrieve_trait_info,
- generate_traits_filename)
+ retrieve_trait_data, retrieve_trait_info)
from gn3.computations.qtlreaper import (
run_reaper,
generate_traits_file,
chromosome_sorter_key_fn,
parse_reaper_main_results,
- organise_reaper_main_results,
- parse_reaper_permutation_results)
+ organise_reaper_main_results)
def export_trait_data(
trait_data: dict, strainlist: Sequence[str], dtype: str = "val",
@@ -159,13 +158,13 @@ def build_heatmap(traits_names, conn: Any):
PARAMETERS:
TODO: Elaborate on the parameters here...
"""
+ # pylint: disable=[R0914]
threshold = 0 # webqtlConfig.PUBLICTHRESH
traits = [
retrieve_trait_info(threshold, fullname, conn)
for fullname in traits_names]
traits_data_list = [retrieve_trait_data(t, conn) for t in traits]
genotype_filename = build_genotype_file(traits[0]["riset"])
- # genotype = parse_genotype_file(genotype_filename)
strains = load_genotype_samples(genotype_filename)
exported_traits_data_list = [
export_trait_data(td, strains) for td in traits_data_list]
@@ -336,6 +335,7 @@ def generate_clustered_heatmap(
Generate a dendrogram, and heatmaps for each chromosome, and put them all
into one plot.
"""
+ # pylint: disable=[R0913, R0914]
num_cols = 1 + len(x_axis)
fig = make_subplots(
rows=1,
@@ -359,14 +359,18 @@ def generate_clustered_heatmap(
"height": 800,
"xaxis": {
"mirror": False,
- "showgrid": True
+ "showgrid": True,
+ "title": x_label
+ },
+ "yaxis": {
+ "title": y_label
}
})
x_axes_layouts = {
"xaxis{}".format(i+1 if i > 0 else ""): {
"mirror": False,
- "showticklabels": True if i == 0 else False,
+ "showticklabels": i == 0,
"ticks": "outside" if i == 0 else ""
}
for i in range(num_cols)}