diff options
Diffstat (limited to 'gn3/heatmaps.py')
| -rw-r--r-- | gn3/heatmaps.py | 28 |
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)} |