diff options
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/heatmap.py | 173 |
1 files changed, 173 insertions, 0 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py new file mode 100644 index 0000000..98ea26f --- /dev/null +++ b/gn3/computations/heatmap.py @@ -0,0 +1,173 @@ +""" +This module will contain functions to be used in computation of the data used to +generate various kinds of heatmaps. +""" + +from gn3.computations.slink import slink +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]["val"]: + sample_data.append(tdata[strain]["val"]) + if var_exists: + if tdata[strain].var: + sample_data.append(tdata[strain]["var"]) + 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): + if tdata.has_key(strain): + if dtype == "val": + return accumulator + (tdata[strain]["val"], ) + if dtype == "var": + return accumulator + (tdata[strain]["var"], ) + if dtype == "N": + return tdata[strain]["ndata"] + if dtype == "all": + return accumulator + __export_all_types( + accumulator, tdata, strain) + else: + raise KeyError("Type `%s` is incorrect" % dtype) + else: + 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(strain), 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()) + else: + 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_j[0] < tdata_i[0]: + corr, nOverlap = compute_correlation(tdata_i, tdata_j) + if (1 - corr) < 0: + return 0.0 + return 1 - corr + return 0.0 + + def __cluster(tdata_i): + res2 = tuple( + __compute_corr(tdata_i, tdata_j) for tdata_j in enumerate(traits)) + + return tuple(__cluster(tdata_i) for tdata_i in enumerate(traits_data_list)) + +def heatmap_data( + fd, search_result, conn: Any, colorScheme=None, userPrivilege=None, + userName=None): + """ + 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... + """ + cluster_checked = fd.formdata.getvalue("clusterCheck", "") + strainlist = [strain for strain in fd.strainlist if strain not in fd.parlist] + genotype = fd.genotype + + def __retrieve_traitlist_and_datalist(threshold, fullname): + trait = retrieve_trait_info(threshold, fullname, conn) + return (trait, export_trait_data(retrieve_trait_data(trait), 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": fd.formdata.getvalue( + "targetDescriptionCheck", ""), + "cluster_checked": cluster_checked, + "slink_data": ( + slink(cluster_traits(traits_list, strainlist)) + if cluster_checked else False) + "sessionfile": fd.formdata.getvalue("session"), + "genotype": genotype, + "nLoci": sum(map(lambda x: len(x), genotype)) + "strainlist": strainlist, + "ppolar": fd.ppolar, + "mpolar":fd.mpolar, + "traits_list": traits_list + "traits_data_list": traits_data_list + } |