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Diffstat (limited to 'gn3/computations/heatmap.py')
| -rw-r--r-- | gn3/computations/heatmap.py | 177 |
1 files changed, 0 insertions, 177 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py deleted file mode 100644 index 3c35029..0000000 --- a/gn3/computations/heatmap.py +++ /dev/null @@ -1,177 +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.db.traits import retrieve_trait_data, retrieve_trait_info -from gn3.computations.correlations2 import compute_correlation - -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 - type: (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(formd, search_result, 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 - cluster_checked = formd.formdata.getvalue("clusterCheck", "") - strainlist = [ - strain for strain in formd.strainlist if strain not in formd.parlist] - genotype = formd.genotype - - def __retrieve_traitlist_and_datalist(threshold, fullname): - trait = retrieve_trait_info(threshold, fullname, conn) - return ( - trait, - export_trait_data(retrieve_trait_data(trait, conn), strainlist)) - - traits_details = [ - __retrieve_traitlist_and_datalist(threshold, fullname) - for fullname in search_result] - traits_list = map(lambda x: x[0], traits_details) - traits_data_list = map(lambda x: x[1], traits_details) - - return { - "target_description_checked": formd.formdata.getvalue( - "targetDescriptionCheck", ""), - "cluster_checked": cluster_checked, - "slink_data": ( - slink(cluster_traits(traits_data_list)) - if cluster_checked else False), - "sessionfile": formd.formdata.getvalue("session"), - "genotype": genotype, - "nLoci": sum(map(len, genotype)), - "strainlist": strainlist, - "ppolar": formd.ppolar, - "mpolar":formd.mpolar, - "traits_list": traits_list, - "traits_data_list": traits_data_list - } |