diff options
| -rw-r--r-- | gn3/api/heatmaps.py | 8 | ||||
| -rw-r--r-- | gn3/app.py | 5 | ||||
| -rw-r--r-- | gn3/computations/qtlreaper.py | 8 | ||||
| -rw-r--r-- | gn3/db/genotypes.py | 1 | ||||
| -rw-r--r-- | gn3/db/traits.py | 2 | ||||
| -rw-r--r-- | gn3/heatmaps.py | 28 |
6 files changed, 37 insertions, 15 deletions
diff --git a/gn3/api/heatmaps.py b/gn3/api/heatmaps.py index 1022a35..fe47aee 100644 --- a/gn3/api/heatmaps.py +++ b/gn3/api/heatmaps.py @@ -1,3 +1,7 @@ +""" +Module to hold the entrypoint functions that generate heatmaps +""" + import io from flask import jsonify from flask import request @@ -9,6 +13,10 @@ heatmaps = Blueprint("heatmaps", __name__) @heatmaps.route("/clustered", methods=("POST",)) def clustered_heatmaps(): + """ + Parses the incoming data and responds with the JSON-serialized plotly figure + representing the clustered heatmap. + """ heatmap_request = request.get_json() traits_names = heatmap_request.get("traits_names", tuple()) if len(traits_names) < 2: @@ -3,7 +3,10 @@ import os from typing import Dict from typing import Union + from flask import Flask +from flask_cors import CORS + from gn3.api.gemma import gemma from gn3.api.rqtl import rqtl from gn3.api.general import general @@ -11,8 +14,6 @@ from gn3.api.heatmaps import heatmaps from gn3.api.correlation import correlation from gn3.api.data_entry import data_entry -from flask_cors import CORS - def create_app(config: Union[Dict, str, None] = None) -> Flask: """Create a new flask object""" app = Flask(__name__) diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py index 377db9b..5d17fed 100644 --- a/gn3/computations/qtlreaper.py +++ b/gn3/computations/qtlreaper.py @@ -87,11 +87,17 @@ def run_reaper( return (output_filename, permu_output_filename) def chromosome_sorter_key_fn(val): + """ + Useful for sorting the chromosomes + """ if isinstance(val, int): return val return ord(val) def organise_reaper_main_results(parsed_results): + """ + Provide the results of running reaper in a format that is easier to use. + """ def __organise_by_chromosome(chr_name, items): chr_items = [item for item in items if item["Chr"] == chr_name] return { @@ -129,12 +135,14 @@ def parse_reaper_main_results(results_file): lines = infile.readlines() def __parse_column_float_value(value): + # pylint: disable=W0702 try: return float(value) except: return value def __parse_column_int_value(value): + # pylint: disable=W0702 try: return int(value) except: diff --git a/gn3/db/genotypes.py b/gn3/db/genotypes.py index 9d052d9..919c539 100644 --- a/gn3/db/genotypes.py +++ b/gn3/db/genotypes.py @@ -115,6 +115,7 @@ def parse_genotype_marker(line: str, geno_obj: dict, parlist: list): Reworks https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/gen_geno_ob.py#L143-L190 """ + # pylint: disable=W0702 marker_row = [item.strip() for item in line.split("\t")] geno_table = { geno_obj["mat"]: -1, geno_obj["pat"]: 1, geno_obj["het"]: 0, diff --git a/gn3/db/traits.py b/gn3/db/traits.py index bfe887e..747ed27 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -46,7 +46,7 @@ def update_sample_data(conn: Any, count: Union[int, str]): """Given the right parameters, update sample-data from the relevant table.""" - # pylint: disable=[R0913, R0914] + # pylint: disable=[R0913, R0914, C0103] STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s" PUBLISH_DATA_SQL: str = ("UPDATE PublishData SET value = %s " "WHERE StrainId = %s AND Id = %s") 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)} |