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-rw-r--r--gn3/computations/heatmap.py173
1 files changed, 173 insertions, 0 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py
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+"""
+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
+ }