diff options
| -rw-r--r-- | gn3/computations/qtlreaper.py | 7 | ||||
| -rw-r--r-- | gn3/db/genotypes.py | 2 | ||||
| -rw-r--r-- | gn3/heatmaps.py | 54 | ||||
| -rw-r--r-- | tests/unit/computations/test_qtlreaper.py | 3 | ||||
| -rw-r--r-- | tests/unit/test_heatmaps.py | 6 |
5 files changed, 32 insertions, 40 deletions
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py index 5180853..377db9b 100644 --- a/gn3/computations/qtlreaper.py +++ b/gn3/computations/qtlreaper.py @@ -110,9 +110,10 @@ def organise_reaper_main_results(parsed_results): unique_chromosomes = {item["Chr"] for item in id_items} return { "ID": identifier, - "chromosomes": {_chr["Chr"]: _chr for _chr in [ - __organise_by_chromosome(chromo, id_items) - for chromo in sorted( + "chromosomes": { + _chr["Chr"]: _chr for _chr in [ + __organise_by_chromosome(chromo, id_items) + for chromo in sorted( unique_chromosomes, key=chromosome_sorter_key_fn)]}} unique_ids = {res["ID"] for res in parsed_results} diff --git a/gn3/db/genotypes.py b/gn3/db/genotypes.py index b03d55c..9d052d9 100644 --- a/gn3/db/genotypes.py +++ b/gn3/db/genotypes.py @@ -174,7 +174,7 @@ def parse_genotype_file(filename: str, parlist: tuple = tuple()): geno_obj = dict(labels + header) markers = tuple( [parse_genotype_marker(line, geno_obj, parlist) - for line in data_lines[1:]]) + for line in data_lines[1:]]) chromosomes = tuple( dict(chromosome) for chromosome in build_genotype_chromosomes(geno_obj, markers)) diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py index 2859dde..c4fc67d 100644 --- a/gn3/heatmaps.py +++ b/gn3/heatmaps.py @@ -3,13 +3,13 @@ This module will contain functions to be used in computation of the data used to generate various kinds of heatmaps. """ +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 gn3.random import random_string -from typing import Any, Dict, Sequence from gn3.computations.slink import slink from plotly.subplots import make_subplots from gn3.computations.correlations2 import compute_correlation @@ -165,7 +165,7 @@ def build_heatmap(traits_names, conn: Any): 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) + # 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] @@ -183,22 +183,21 @@ def build_heatmap(traits_names, conn: Any): [t[2] for t in strains_and_values], traits_filename) - main_output, permutations_output = run_reaper( + main_output, _permutations_output = run_reaper( genotype_filename, traits_filename, separate_nperm_output=True) qtlresults = parse_reaper_main_results(main_output) - permudata = parse_reaper_permutation_results(permutations_output) + # permudata = parse_reaper_permutation_results(permutations_output) organised = organise_reaper_main_results(qtlresults) traits_ids = [# sort numerically, but retain the ids as strings str(i) for i in sorted({int(row["ID"]) for row in qtlresults})] chromosome_names = sorted( - {row["Chr"] for row in qtlresults}, key = chromosome_sorter_key_fn) - loci_names = sorted({row["Locus"] for row in qtlresults}) - ordered_traits_names = { - res_id: trait for res_id, trait in + {row["Chr"] for row in qtlresults}, key=chromosome_sorter_key_fn) + # loci_names = sorted({row["Locus"] for row in qtlresults}) + ordered_traits_names = dict( zip(traits_ids, - [traits[idx]["trait_fullname"] for idx in traits_order])} + [traits[idx]["trait_fullname"] for idx in traits_order])) return generate_clustered_heatmap( process_traits_data_for_heatmap( @@ -207,22 +206,11 @@ def build_heatmap(traits_names, conn: Any): "single_heatmap_{}".format(random_string(10)), y_axis=tuple( ordered_traits_names[traits_ids[order]] - for order in traits_order), + for order in traits_order), y_label="Traits", - x_axis=[chromo for chromo in chromosome_names], + x_axis=chromosome_names, x_label="Chromosomes") - return { - "slink_data": slink_data, - "ordering_data": ordering_data, - "strainlist": strainlist, - "genotype_filename": genotype_filename, - "traits_list": traits_list, - "traits_data_list": traits_data_list, - "exported_traits_data_list": exported_traits_data_list, - "traits_filename": traits_filename - } - def compute_traits_order(slink_data, neworder: tuple = tuple()): """ Compute the order of the traits for clustering from `slink_data`. @@ -314,7 +302,7 @@ def get_nearest_marker(traits_list, genotype): https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L419-L438 """ if not genotype["Mbmap"]: - return [None] * len(trait_list) + return [None] * len(traits_list) marker_finder = nearest_marker_finder(genotype) return [marker_finder(trait) for trait in traits_list] @@ -340,10 +328,10 @@ def process_traits_data_for_heatmap(data, trait_names, chromosome_names): return hdata def generate_clustered_heatmap( - data, clustering_data, image_filename_prefix, x_axis = None, - x_label: str = "", y_axis = None, y_label: str = "", + data, clustering_data, image_filename_prefix, x_axis=None, + x_label: str = "", y_axis=None, y_label: str = "", output_dir: str = TMPDIR, - colorscale = ( + colorscale=( (0.0, '#5D5D5D'), (0.4999999999999999, '#ABABAB'), (0.5, '#F5DE11'), (1.0, '#FF0D00'))): """ @@ -357,15 +345,15 @@ def generate_clustered_heatmap( shared_yaxes="rows", horizontal_spacing=0.001, subplot_titles=["distance"] + x_axis, - figure = ff.create_dendrogram( + figure=ff.create_dendrogram( np.array(clustering_data), orientation="right", labels=y_axis)) hms = [go.Heatmap( name=chromo, - y = y_axis, - z = data_array, + y=y_axis, + z=data_array, showscale=False) for chromo, data_array in zip(x_axis, data)] - for i, hm in enumerate(hms): - fig.add_trace(hm, row=1, col=(i + 2)) + for i, heatmap in enumerate(hms): + fig.add_trace(heatmap, row=1, col=(i + 2)) fig.update_layout( { @@ -380,8 +368,8 @@ def generate_clustered_heatmap( x_axes_layouts = { "xaxis{}".format(i+1 if i > 0 else ""): { "mirror": False, - "showticklabels": True if i==0 else False, - "ticks": "outside" if i==0 else "" + "showticklabels": True if i == 0 else False, + "ticks": "outside" if i == 0 else "" } for i in range(num_cols)} diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py index 1d67827..d420470 100644 --- a/tests/unit/computations/test_qtlreaper.py +++ b/tests/unit/computations/test_qtlreaper.py @@ -77,6 +77,7 @@ class TestQTLReaper(TestCase): 5.82775, 5.89659, 5.92117, 5.93396, 5.93396, 5.94957]) def test_organise_reaper_main_results(self): + """Check that results are organised correctly.""" self.assertEqual( organise_reaper_main_results([ { @@ -135,7 +136,7 @@ class TestQTLReaper(TestCase): 1: {"Chr": 1, "loci": [ { - "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010, + "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010, "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 }, { diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py index f3a81c5..c0a496b 100644 --- a/tests/unit/test_heatmaps.py +++ b/tests/unit/test_heatmaps.py @@ -189,6 +189,7 @@ class TestHeatmap(TestCase): retrieve_strains_and_values(orders, slist, tdata), expected) def test_get_lrs_from_chr(self): + """Check that function gets correct LRS values""" for trait, chromosome, expected in [ [{"chromosomes": {}}, 3, [None]], [{"chromosomes": {3: {"loci": [ @@ -202,6 +203,7 @@ class TestHeatmap(TestCase): self.assertEqual(get_lrs_from_chr(trait, chromosome), expected) def test_process_traits_data_for_heatmap(self): + """Check for correct processing of data for heatmap generation.""" self.assertEqual( process_traits_data_for_heatmap( {"1": { @@ -210,7 +212,7 @@ class TestHeatmap(TestCase): 1: {"Chr": 1, "loci": [ { - "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010, + "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010, "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 }, { @@ -257,7 +259,7 @@ class TestHeatmap(TestCase): 1: {"Chr": 1, "loci": [ { - "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010, + "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010, "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 }, { |