From 9631e6f2e4b7f304ad1a4b7d3ee4ebe9980ce926 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 23 Sep 2019 14:03:30 -0400
Subject: [PATCH] update
---
docs/generate_class1_pan.py | 75 ++++++++++---------
...test_released_predictors_on_hpv_dataset.py | 3 +
2 files changed, 42 insertions(+), 36 deletions(-)
diff --git a/docs/generate_class1_pan.py b/docs/generate_class1_pan.py
index 7e70cada..af81ed36 100644
--- a/docs/generate_class1_pan.py
+++ b/docs/generate_class1_pan.py
@@ -36,13 +36,13 @@ parser.add_argument(
)
parser.add_argument(
"--logo-cutoff",
- default=0.001,
+ default=0.01,
type=float,
help="Fraction of top to use for motifs",
)
parser.add_argument(
"--length-cutoff",
- default=0.0001,
+ default=0.01,
type=float,
help="Fraction of top to use for length distribution",
)
@@ -104,34 +104,39 @@ def model_info(models_dir):
def write_logo(
normalized_frequency_matrices,
allele,
- length,
+ lengths,
cutoff,
models_label,
out_dir):
- matrix = normalized_frequency_matrices.loc[
- (normalized_frequency_matrices.allele == allele) &
- (normalized_frequency_matrices.length == length) &
- (normalized_frequency_matrices.cutoff_fraction == cutoff)
- ].set_index("position")[AMINO_ACIDS]
- if matrix.shape[0] == 0:
- return None
- matrix = (matrix.T / matrix.sum(1)).T # row normalize
-
- fig = pyplot.figure(figsize=(8,4))
- ss_logo = logomaker.Logo(
- matrix,
- width=.8,
- vpad=.05,
- fade_probabilities=True,
- stack_order='small_on_top',
- # color_scheme='dodgerblue',
- # ax=ax,
- )
- pyplot.title("%s %d-mer (%s)" % (allele, length, models_label))
- pyplot.xticks(matrix.index.values)
- name = "%s-%dmer.%s.png" % (
- allele.replace("*", "-").replace(":", "-"), length, models_label)
+ fig = pyplot.figure(figsize=(8,10))
+
+ for (i, length) in enumerate(lengths):
+ ax = pyplot.subplot(len(lengths), 1, i + 1)
+ matrix = normalized_frequency_matrices.loc[
+ (normalized_frequency_matrices.allele == allele) &
+ (normalized_frequency_matrices.length == length) &
+ (normalized_frequency_matrices.cutoff_fraction == cutoff)
+ ].set_index("position")[AMINO_ACIDS]
+ if matrix.shape[0] == 0:
+ return None
+
+ matrix = (matrix.T / matrix.sum(1)).T # row normalize
+
+ ss_logo = logomaker.Logo(
+ matrix,
+ width=.8,
+ vpad=.05,
+ fade_probabilities=True,
+ stack_order='small_on_top',
+ ax=ax,
+ )
+ pyplot.title(
+ "%s %d-mer (%s)" % (allele, length, models_label), y=0.85)
+ pyplot.xticks(matrix.index.values)
+ pyplot.tight_layout()
+ name = "%s.motifs.%s.png" % (
+ allele.replace("*", "-").replace(":", "-"), models_label)
filename = os.path.abspath(join(out_dir, name))
pyplot.savefig(filename)
print("Wrote: ", filename)
@@ -244,16 +249,14 @@ def go(argv):
info['observations_per_allele'].get(allele, 0)))
w("\n")
w(image(length_distribution_image_path))
-
- for length in args.motif_lengths:
- w(image(write_logo(
- normalized_frequency_matrices=normalized_frequency_matrices,
- allele=allele,
- length=length,
- cutoff=args.logo_cutoff,
- out_dir=args.out_dir,
- models_label=label,
- )))
+ w(image(write_logo(
+ normalized_frequency_matrices=normalized_frequency_matrices,
+ allele=allele,
+ lengths=args.motif_lengths,
+ cutoff=args.logo_cutoff,
+ out_dir=args.out_dir,
+ models_label=label,
+ )))
w("")
document_path = join(args.out_dir, "allele_motifs.rst")
diff --git a/test/test_released_predictors_on_hpv_dataset.py b/test/test_released_predictors_on_hpv_dataset.py
index 26bf0227..25be5823 100644
--- a/test/test_released_predictors_on_hpv_dataset.py
+++ b/test/test_released_predictors_on_hpv_dataset.py
@@ -61,6 +61,9 @@ def test_on_hpv(df=DF):
scores_df = scores_df.pivot(
index="metric", columns="predictor", values="score")
+ print("Predictions")
+ print(df)
+
print("Scores")
print(scores_df)
--
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