diff options
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/heatmap.py | 277 |
1 files changed, 0 insertions, 277 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py deleted file mode 100644 index 8727c92..0000000 --- a/gn3/computations/heatmap.py +++ /dev/null @@ -1,277 +0,0 @@ -""" -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 -from gn3.computations.slink import slink -from gn3.computations.qtlreaper import generate_traits_file -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, - generate_traits_filename) - -def export_trait_data( - trait_data: dict, strainlist: Sequence[str], dtype: str = "val", - var_exists: bool = False, n_exists: bool = False): - """ - Export data according to `strainlist`. Mostly used in calculating - correlations. - - DESCRIPTION: - Migrated from - https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L166-L211 - - PARAMETERS - trait: (dict) - The dictionary of key-value pairs representing a trait - strainlist: (list) - A list of strain names - dtype: (str) - ... verify what this is ... - var_exists: (bool) - A flag indicating existence of variance - n_exists: (bool) - A flag indicating existence of ndata - """ - def __export_all_types(tdata, strain): - sample_data = [] - if tdata[strain]["value"]: - sample_data.append(tdata[strain]["value"]) - if var_exists: - if tdata[strain]["variance"]: - sample_data.append(tdata[strain]["variance"]) - else: - sample_data.append(None) - if n_exists: - if tdata[strain]["ndata"]: - sample_data.append(tdata[strain]["ndata"]) - else: - sample_data.append(None) - else: - if var_exists and n_exists: - sample_data += [None, None, None] - elif var_exists or n_exists: - sample_data += [None, None] - else: - sample_data.append(None) - - return tuple(sample_data) - - def __exporter(accumulator, strain): - # pylint: disable=[R0911] - if strain in trait_data["data"]: - if dtype == "val": - return accumulator + (trait_data["data"][strain]["value"], ) - if dtype == "var": - return accumulator + (trait_data["data"][strain]["variance"], ) - if dtype == "N": - return accumulator + (trait_data["data"][strain]["ndata"], ) - if dtype == "all": - return accumulator + __export_all_types(trait_data["data"], strain) - raise KeyError("Type `%s` is incorrect" % dtype) - if var_exists and n_exists: - return accumulator + (None, None, None) - if var_exists or n_exists: - return accumulator + (None, None) - return accumulator + (None,) - - return reduce(__exporter, strainlist, tuple()) - -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 "%s::%s" % ( - trait["db"]["displayname"], - desc[desc.rindex(':')+1:].strip()) - return "%s::%s" % ( - trait["db"]["displayname"], - desc[:desc.index('entered')].strip()) - prefix = "%s::%s" % ( - trait["db"]["dataset_name"], trait["trait_name"]) - if trait["cellid"]: - return "%s::%s" % (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 - corr_vals = compute_correlation(tdata_i[1], tdata_j[1]) - corr = corr_vals[0] - if (1 - corr) < 0: - return 0.0 - return 1 - corr - - 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 heatmap_data(traits_names, conn: Any): - """ - 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... - """ - threshold = 0 # webqtlConfig.PUBLICTHRESH - def __retrieve_traitlist_and_datalist(threshold, fullname): - trait = retrieve_trait_info(threshold, fullname, conn) - return (trait, retrieve_trait_data(trait, conn)) - - traits_details = [ - __retrieve_traitlist_and_datalist(threshold, fullname) - for fullname in traits_names] - traits_list = tuple(x[0] for x in traits_details) - traits_data_list = [x[1] for x in traits_details] - genotype_filename = build_genotype_file(traits_list[0]["riset"]) - strainlist = load_genotype_samples(genotype_filename) - exported_traits_data_list = tuple( - export_trait_data(td, strainlist) for td in traits_data_list) - slink_data = slink(cluster_traits(exported_traits_data_list)) - ordering_data = compute_heatmap_order(slink_data) - strains_and_values = retrieve_strains_and_values( - ordering_data, strainlist, exported_traits_data_list) - strains_values = strains_and_values[0][1] - trait_values = [t[2] for t in strains_and_values] - traits_filename = generate_traits_filename() - generate_traits_file(strains_values, trait_values, traits_filename) - - 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`. - - 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_strains_and_values(orders, strainlist, traits_data_list): - """ - Get the strains and their corresponding values from `strainlist` 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 - strains = [] - values = [] - rets = [] - for order in orders: - temp_val = traits_data_list[order] - for i, strain in enumerate(strainlist): - if temp_val[i] is not None: - strains.append(strain) - values.append(temp_val[i]) - rets.append([order, strains[:], values[:]]) - strains = [] - 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(trait_list) - - marker_finder = nearest_marker_finder(genotype) - return [marker_finder(trait) for trait in traits_list] |