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authorFrederick Muriuki Muriithi2021-09-16 11:36:42 +0300
committerFrederick Muriuki Muriithi2021-09-16 11:36:42 +0300
commit2cc9f382e199dbdbaab98c7e06deabd72e244adb (patch)
treed0deef01db734d4c702642370a4cbb28eb43301f
parent78e37440844a0397d29135a8ba215e54fd92c86d (diff)
downloadgenenetwork3-2cc9f382e199dbdbaab98c7e06deabd72e244adb.tar.gz
Fix minor bugs
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix a few minor bugs left over from the integration of code from the proof-of-concept code.
-rw-r--r--gn3/heatmaps.py8
1 files changed, 4 insertions, 4 deletions
diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py
index c48a2d3..170b0cd 100644
--- a/gn3/heatmaps.py
+++ b/gn3/heatmaps.py
@@ -160,7 +160,7 @@ def build_heatmap(traits_names, conn: Any):
threshold = 0 # webqtlConfig.PUBLICTHRESH
traits = [
retrieve_trait_info(threshold, fullname, conn)
- for fullname in trait_fullnames()]
+ for fullname in traits_names]
traits_data_list = [retrieve_trait_data(t, conn) for t in traits]
genotype_filename = build_genotype_file(traits[0]["riset"])
genotype = parse_genotype_file(genotype_filename)
@@ -338,9 +338,9 @@ def process_traits_data_for_heatmap(data, trait_names, chromosome_names):
def generate_clustered_heatmap(
data, image_filename_prefix, x_axis = None, x_label: str = "",
y_axis = None, y_label: str = "", output_dir: str = TMPDIR,
- colorscale = [
- [0.0, '#3B3B3B'], [0.4999999999999999, '#ABABAB'],
- [0.5, '#F5DE11']], [1.0, '#FF0D00']):
+ colorscale = (
+ (0.0, '#3B3B3B'), (0.4999999999999999, '#ABABAB'),
+ (0.5, '#F5DE11'), (1.0, '#FF0D00'))):
"""
Generate a dendrogram, and heatmaps for each chromosome, and put them all
into one plot.