"""
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, Union, Sequence
import numpy as np
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.random import random_string
from gn3.computations.slink import slink
from gn3.db.traits import export_trait_data
from gn3.computations.correlations2 import compute_correlation
from gn3.db.genotypes import (
build_genotype_file, load_genotype_samples)
from gn3.db.traits import (
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)
def trait_display_name(trait: Dict):
"""
Given a trait, return a name to use to display the trait on a heatmap.
DESCRIPTION
Migrated from
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L141-L157
"""
if trait.get("db", None) and trait.get("trait_name", None):
if trait["db"]["dataset_type"] == "Temp":
desc = trait["description"]
if desc.find("PCA") >= 0:
return (
f'{trait["db"]["displayname"]}::'
f'{desc[desc.rindex(":")+1:].strip()}')
return (
f'{trait["db"]["displayname"]}::'
f'{desc[:desc.index("entered")].strip()}')
prefix = f'{trait["db"]["dataset_name"]}::{trait["trait_name"]}'
if trait["cellid"]:
return '{prefix}::{trait["cellid"]}'
return prefix
return trait["description"]
def cluster_traits(traits_data_list: Sequence[Dict]):
"""
Clusters the trait values.
DESCRIPTION
Attempts to replicate the clustering of the traits, as done at
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L138-L162
"""
def __compute_corr(tdata_i, tdata_j):
if tdata_i[0] == tdata_j[0]:
return 0.0
return 1 - compute_correlation(tdata_i[1], tdata_j[1])[0]
def __cluster(tdata_i):
return tuple(
__compute_corr(tdata_i, tdata_j)
for tdata_j in enumerate(traits_data_list))
return tuple(__cluster(tdata_i) for tdata_i in enumerate(traits_data_list))
def get_loci_names(
organised: dict,
chromosome_names: Sequence[str]) -> Sequence[Sequence[str]]:
"""
Get the loci names organised by the same order as the `chromosome_names`.
"""
def __get_trait_loci(accumulator, trait):
chrs = tuple(trait["chromosomes"].keys())
trait_loci = {
_chr: tuple(
locus["Locus"]
for locus in trait["chromosomes"][_chr]["loci"]
) for _chr in chrs
}
return {
**accumulator,
**{
_chr: tuple(sorted(set(
trait_loci[_chr] + accumulator.get(_chr, tuple()))))
for _chr in trait_loci.keys()
}
}
loci_dict: Dict[Union[str, int], Sequence[str]] = reduce(
__get_trait_loci, [v[1] for v in organised.items()], {})
return tuple(loci_dict[_chr] for _chr in chromosome_names)
def build_heatmap(
traits_names: Sequence[str], conn: Any,
vertical: bool = False) -> go.Figure:
"""
heatmap function
DESCRIPTION
This function is an attempt to reproduce the initialisation at
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L46-L64
and also the clustering and slink computations at
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L138-L165
with the help of the `gn3.computations.heatmap.cluster_traits` function.
It does not try to actually draw the heatmap image.
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]["group"])
samples = load_genotype_samples(genotype_filename)
exported_traits_data_list = [
export_trait_data(td, samples) for td in traits_data_list]
clustered = cluster_traits(exported_traits_data_list)
slinked = slink(clustered)
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"
generate_traits_file(
samples_and_values[0][1],
[t[2] for t in samples_and_values],
traits_filename)
main_output, _permutations_output = run_reaper(
genotype_filename, traits_filename, separate_nperm_output=True)
qtlresults = parse_reaper_main_results(main_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)
ordered_traits_names = dict(
zip(traits_ids,
[traits[idx]["trait_fullname"] for idx in traits_order]))
return clustered_heatmap(
process_traits_data_for_heatmap(
organised, traits_ids, chromosome_names),
clustered,
x_axis={
"label": "Chromosomes",
"data": chromosome_names
},
y_axis={
"label": "Traits",
"data": tuple(
ordered_traits_names[traits_ids[order]]
for order in traits_order)
},
vertical=vertical,
loci_names=get_loci_names(organised, chromosome_names))
def compute_traits_order(slink_data, neworder: tuple = tuple()):
"""
Compute the order of the traits for clustering from `slink_data`.
This function tries to reproduce the creation and update of the `neworder`
variable in
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L120
and in the `web.webqtl.heatmap.Heatmap.draw` function in GN1
"""
def __order_maker(norder, slnk_dt):
if isinstance(slnk_dt[0], int) and isinstance(slnk_dt[1], int):
return norder + (slnk_dt[0], slnk_dt[1])
if isinstance(slnk_dt[0], int):
return __order_maker((norder + (slnk_dt[0], )), slnk_dt[1])
if isinstance(slnk_dt[1], int):
return __order_maker(norder, slnk_dt[0]) + (slnk_dt[1], )
return __order_maker(__order_maker(norder, slnk_dt[0]), slnk_dt[1])
return __order_maker(neworder, slink_data)
def retrieve_samples_and_values(orders, samplelist, traits_data_list):
"""
Get the samples and their corresponding values from `samplelist` and
`traits_data_list`.
This migrates the code in
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L215-221
"""
# This feels nasty! There's a lot of mutation of values here, that might
# indicate something untoward in the design of this function and its
# dependents ==> Review
samples = []
values = []
rets = []
for order in orders:
temp_val = traits_data_list[order]
for i, sample in enumerate(samplelist):
if temp_val[i] is not None:
samples.append(sample)
values.append(temp_val[i])
rets.append([order, samples[:], values[:]])
samples = []
values = []
return rets
def nearest_marker_finder(genotype):
"""
Returns a function to be used with `genotype` to compute the nearest marker
to the trait passed to the returned function.
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L425-434
"""
def __compute_distances(chromo, trait):
loci = chromo.get("loci", None)
if not loci:
return None
return tuple(
{
"name": locus["name"],
"distance": abs(locus["Mb"] - trait["mb"])
} for locus in loci)
def __finder(trait):
_chrs = tuple(
_chr for _chr in genotype["chromosomes"]
if str(_chr["name"]) == str(trait["chr"]))
if len(_chrs) == 0:
return None
distances = tuple(
distance for dists in
filter(
lambda x: x is not None,
(__compute_distances(_chr, trait) for _chr in _chrs))
for distance in dists)
nearest = min(distances, key=lambda d: d["distance"])
return nearest["name"]
return __finder
def get_nearest_marker(traits_list, genotype):
"""
Retrieves the nearest marker for each of the traits in the list.
DESCRIPTION:
This migrates the code in
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L419-L438
"""
if not genotype["Mbmap"]:
return [None] * len(traits_list)
marker_finder = nearest_marker_finder(genotype)
return [marker_finder(trait) for trait in traits_list]
def get_lrs_from_chr(trait, chr_name):
"""
Retrieve the LRS values for a specific chromosome in the given trait.
"""
chromosome = trait["chromosomes"].get(chr_name)
if chromosome:
return [
locus["LRS"] for locus in
sorted(chromosome["loci"], key=lambda loc: loc["Locus"])]
return [None]
def process_traits_data_for_heatmap(data, trait_names, chromosome_names):
"""
Process the traits data in a format useful for generating heatmap diagrams.
"""
hdata = [
[get_lrs_from_chr(data[trait], chr_name) for trait in trait_names]
for chr_name in chromosome_names]
return hdata
def clustered_heatmap(
data: Sequence[Sequence[float]], clustering_data: Sequence[float],
x_axis,#: Dict[Union[str, int], Union[str, Sequence[str]]],
y_axis: Dict[str, Union[str, Sequence[str]]],
loci_names: Sequence[Sequence[str]] = tuple(),
vertical: bool = False,
colorscale: Sequence[Sequence[Union[float, str]]] = (
(0.0, '#0000FF'), (0.5, '#00FF00'), (1.0, '#FF0000'))) -> go.Figure:
"""
Generate a dendrogram, and heatmaps for each chromosome, and put them all
into one plot.
"""
# pylint: disable=[R0913, R0914]
x_axis_data = x_axis["data"]
y_axis_data = y_axis["data"]
num_plots = 1 + len(x_axis_data)
fig = make_subplots(
rows=num_plots if vertical else 1,
cols=1 if vertical else num_plots,
shared_xaxes="columns" if vertical else False,
shared_yaxes=False if vertical else "rows",
vertical_spacing=0.010,
horizontal_spacing=0.001,
subplot_titles=["" if vertical else x_axis["label"]] + [
f"Chromosome: {chromo}" if vertical else chromo
for chromo in x_axis_data],#+ x_axis_data,
figure=ff.create_dendrogram(
np.array(clustering_data),
orientation="bottom" if vertical else "right",
labels=y_axis_data))
hms = [go.Heatmap(
name=chromo,
x=y_axis_data if vertical else loci,
y=loci if vertical else y_axis_data,
z=data_array,
transpose=vertical,
showscale=False)
for chromo, data_array, loci
in zip(x_axis_data, data, loci_names)]
for i, heatmap in enumerate(hms):
fig.add_trace(
heatmap,
row=((i + 2) if vertical else 1),
col=(1 if vertical else (i + 2)))
axes_layouts = {
"{axis}axis{count}".format( # pylint: disable=[C0209]
axis=("y" if vertical else "x"),
count=(i+1 if i > 0 else "")): {
"mirror": False,
"showticklabels": i == 0,
"ticks": "outside" if i == 0 else ""
}
for i in range(num_plots)}
fig.update_layout({
"width": 800 if vertical else 4000,
"height": 4000 if vertical else 800,
"{}axis".format("x" if vertical else "y"): { # pylint: disable=[C0209]
"mirror": False,
"ticks": "",
"side": "top" if vertical else "left",
"title": y_axis["label"],
"tickangle": 90 if vertical else 0,
"ticklabelposition": "outside top" if vertical else "outside left"
},
"{}axis".format("y" if vertical else "x"): { # pylint: disable=[C0209]
"mirror": False,
"showgrid": True,
"title": "Distance",
"side": "right" if vertical else "top"
},
**axes_layouts})
fig.update_traces(
showlegend=False,
colorscale=colorscale,
selector={"type": "heatmap"})
fig.update_traces(
showlegend=True,
showscale=True,
selector={"name": x_axis_data[-1]})
return fig
