diff options
| -rw-r--r-- | gn3/api/heatmaps.py | 6 | ||||
| -rw-r--r-- | gn3/heatmaps.py | 14 |
2 files changed, 13 insertions, 7 deletions
diff --git a/gn3/api/heatmaps.py b/gn3/api/heatmaps.py index 26c165f..1b04a95 100644 --- a/gn3/api/heatmaps.py +++ b/gn3/api/heatmaps.py @@ -31,7 +31,11 @@ def clustered_heatmaps(): traits_fullnames = [parse_trait_fullname(trait) for trait in traits_names] with io.StringIO() as io_str: - figure = build_heatmap(traits_fullnames, conn, vertical=vertical) + figure = build_heatmap(conn, + traits_fullnames, + current_app.config["GENOTYPE_FILES"], + vertical=vertical, + current_app.config["TMPDIR"]) figure.write_json(io_str) fig_json = io_str.getvalue() return fig_json, 200 diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py index 882a3c7..79c4082 100644 --- a/gn3/heatmaps.py +++ b/gn3/heatmaps.py @@ -2,7 +2,7 @@ This module will contain functions to be used in computation of the data used to generate various kinds of heatmaps. """ - +from pathlib import Path from functools import reduce from typing import Any, Dict, Union, Sequence @@ -11,7 +11,6 @@ import plotly.graph_objects as go # type: ignore import plotly.figure_factory as ff # type: ignore from plotly.subplots import make_subplots # type: ignore -from gn3.settings import TMPDIR from gn3.chancy import random_string from gn3.computations.slink import slink from gn3.db.traits import export_trait_data @@ -99,8 +98,11 @@ def get_loci_names( return tuple(loci_dict[_chr] for _chr in chromosome_names) def build_heatmap( - traits_names: Sequence[str], conn: Any, - vertical: bool = False) -> go.Figure: + conn: Any, + traits_names: Sequence[str], + genotype_files: Union[str, Path], + vertical: bool = False, + tmpdir: Union[str, Path] = "/tmp") -> go.Figure: """ heatmap function @@ -122,7 +124,7 @@ def build_heatmap( 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]["group"]) + genotype_filename = build_genotype_file(traits[0]["group"], genotype_files) samples = load_genotype_samples(genotype_filename) exported_traits_data_list = [ export_trait_data(td, samples) for td in traits_data_list] @@ -131,7 +133,7 @@ def build_heatmap( traits_order = compute_traits_order(slinked) samples_and_values = retrieve_samples_and_values( traits_order, samples, exported_traits_data_list) - traits_filename = f"{TMPDIR}/traits_test_file_{random_string(10)}.txt" + traits_filename = f"{tmpdir}/traits_test_file_{random_string(10)}.txt" generate_traits_file( samples_and_values[0][1], [t[2] for t in samples_and_values], |