From 384dab34b89fdf8baa0066b24c550911d2e8cf3b Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 20 Sep 2019 14:21:25 -0400
Subject: [PATCH] better docs
---
docs/generate_class1_pan.py | 46 ++++++++++++++++++++++++++++---------
1 file changed, 35 insertions(+), 11 deletions(-)
diff --git a/docs/generate_class1_pan.py b/docs/generate_class1_pan.py
index 080421fe..7e70cada 100644
--- a/docs/generate_class1_pan.py
+++ b/docs/generate_class1_pan.py
@@ -5,6 +5,7 @@ from __future__ import print_function
import sys
import argparse
from collections import OrderedDict, defaultdict
+import os
from os.path import join, exists
from os import mkdir
@@ -35,7 +36,7 @@ parser.add_argument(
)
parser.add_argument(
"--logo-cutoff",
- default=0.01,
+ default=0.001,
type=float,
help="Fraction of top to use for motifs",
)
@@ -46,10 +47,18 @@ parser.add_argument(
help="Fraction of top to use for length distribution",
)
parser.add_argument(
- "--lengths",
+ "--length-distribution-lengths",
+ nargs="+",
+ default=[8, 9, 10, 11, 12, 13, 14, 15],
+ type=int,
+ help="Peptide lengths for length distribution plots",
+)
+parser.add_argument(
+ "--motif-lengths",
+ nargs="+",
default=[8, 9, 10, 11],
type=int,
- help="Peptide lengths",
+ help="Peptide lengths for motif plots",
)
parser.add_argument(
"--out-dir",
@@ -59,6 +68,7 @@ parser.add_argument(
)
parser.add_argument(
"--max-alleles",
+ default=None,
type=int,
metavar="N",
help="Only use N alleles (for testing)",
@@ -70,6 +80,8 @@ def model_info(models_dir):
join(models_dir, "length_distributions.csv.bz2"))
frequency_matrices_df = pandas.read_csv(
join(models_dir, "frequency_matrices.csv.bz2"))
+ train_data_df = pandas.read_csv(
+ join(models_dir, "train_data.csv.bz2"))
distribution = frequency_matrices_df.loc[
(frequency_matrices_df.cutoff_fraction == 1.0), AMINO_ACIDS
@@ -79,9 +91,13 @@ def model_info(models_dir):
normalized_frequency_matrices.loc[:, AMINO_ACIDS] = (
normalized_frequency_matrices[AMINO_ACIDS] / distribution)
+ observations_per_allele = (
+ train_data_df.groupby("allele").peptide.nunique().to_dict())
+
return {
'length_distributions': length_distributions_df,
'normalized_frequency_matrices': normalized_frequency_matrices,
+ 'observations_per_allele': observations_per_allele,
}
@@ -114,9 +130,11 @@ def write_logo(
)
pyplot.title("%s %d-mer (%s)" % (allele, length, models_label))
pyplot.xticks(matrix.index.values)
- name = "%s_%dmer.%s.png" % (allele, length, models_label)
- pyplot.savefig(join(out_dir, name))
- print("Wrote: ", name)
+ name = "%s-%dmer.%s.png" % (
+ allele.replace("*", "-").replace(":", "-"), length, models_label)
+ filename = os.path.abspath(join(out_dir, name))
+ pyplot.savefig(filename)
+ print("Wrote: ", filename)
fig.clear()
pyplot.close(fig)
return name
@@ -140,9 +158,12 @@ def write_length_distribution(
pyplot.xlabel("")
pyplot.xticks(rotation=0)
pyplot.gca().get_legend().remove()
- name = "%s.lengths.%s.png" % (allele, models_label)
- pyplot.savefig(join(out_dir, name))
- print("Wrote: ", name)
+ name = "%s.lengths.%s.png" % (
+ allele.replace("*", "-").replace(":", "-"), models_label)
+
+ filename = os.path.abspath(join(out_dir, name))
+ pyplot.savefig(filename)
+ print("Wrote: ", filename)
fig.clear()
pyplot.close(fig)
return name
@@ -208,7 +229,7 @@ def go(argv):
length_distribution_image_path = write_length_distribution(
length_distributions_df=length_distribution,
allele=allele,
- lengths=args.lengths,
+ lengths=args.length_distribution_lengths,
cutoff=args.length_cutoff,
out_dir=args.out_dir,
models_label=label)
@@ -219,9 +240,12 @@ def go(argv):
"*" + (
"With mass-spec" if label == "with_mass_spec" else "Affinities only")
+ "*\n")
+ w("Training observations (unique peptides): %d" % (
+ info['observations_per_allele'].get(allele, 0)))
+ w("\n")
w(image(length_distribution_image_path))
- for length in args.lengths:
+ for length in args.motif_lengths:
w(image(write_logo(
normalized_frequency_matrices=normalized_frequency_matrices,
allele=allele,
--
GitLab