diff options
Diffstat (limited to 'gn3/computations/heatmap.py')
| -rw-r--r-- | gn3/computations/heatmap.py | 7 |
1 files changed, 4 insertions, 3 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py index 92014cf..1143450 100644 --- a/gn3/computations/heatmap.py +++ b/gn3/computations/heatmap.py @@ -6,6 +6,7 @@ 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 ( @@ -155,14 +156,14 @@ def heatmap_data(traits_names, conn: Any): 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] - exported_traits_data_list = tuple( - export_trait_data(td, strainlist) for td in traits_data_list) 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( - orders, strainlist, exported_traits_data_list) + 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() |