def make_gene_sig_clustergram():
if request.method == 'POST':
post_data = json.loads(request.data)
uids = post_data.get('ids', '')
genes = post_data.get('genes', '')
genes = map(lambda x: x.upper(), genes)
na_val = post_data.get('na_val', 0)
mat = get_matrix(uids, genes, na_val=na_val)
json_data = clustergram.clustergram(mat, genes, uids)
return json.dumps(json_data)
import os, sys, json
from clustergram import clustergram
from orm_utils import *
sys.path.append('../../maayanlab_utils')
from fileIO import read_df
def find_name_for_id(uid):
projection = {'_id':False, 'limma':False, 'fold_changes':False, 'chdir': False}
dbs = DBSignature(uid,projection)
return dbs.name + '|' + dbs.meta['geo_id']
# mat, ids, _ = read_df('../signed_jaccard_subset_unique_entries_831x831.txt')
# mat, ids, _ = read_df('../signed_jaccard_subset_unique_entries_519x519.txt')
mat, ids, _ = read_df('../signed_jaccard_subset_unique_entries_259x259.txt')
names = map(find_name_for_id, ids)
json_data = clustergram(mat, names, names,
row_linkage='average', col_linkage='average',
row_pdist='cosine', col_pdist='cosine')
json.dump(json_data, open('/Library/WebServer/Documents/d3_clustergram/signed_jaccard_subset_clustergram_259.json', 'wb'))
def find_name_for_id(uid):
projection = {
'_id': False,
'limma': False,
'fold_changes': False,
'chdir': False
}
dbs = DBSignature(uid, projection)
return dbs.name + '|' + dbs.meta['geo_id']
# mat, ids, _ = read_df('../signed_jaccard_subset_unique_entries_831x831.txt')
# mat, ids, _ = read_df('../signed_jaccard_subset_unique_entries_519x519.txt')
mat, ids, _ = read_df('../signed_jaccard_subset_unique_entries_259x259.txt')
names = map(find_name_for_id, ids)
json_data = clustergram(mat,
names,
names,
row_linkage='average',
col_linkage='average',
row_pdist='cosine',
col_pdist='cosine')
json.dump(
json_data,
open(
'/Library/WebServer/Documents/d3_clustergram/signed_jaccard_subset_clustergram_259.json',
'wb'))