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[ADD] Add pi0estimation extended error help into separate PR from PR … #103

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Mar 25, 2022
Merged

[ADD] Add pi0estimation extended error help into separate PR from PR … #103

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11 changes: 10 additions & 1 deletion pyprophet/report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,4 +137,13 @@ def plot_scores(df, out, color_palette="normal"):
plt.subplot(212)

pdf.savefig()
plt.close()
plt.close()

def plot_hist(x, title, xlabel, ylabel, pdf_path="histogram_plot.png"):

if plt is not None:
counts, __, __ = plt.hist(x, bins=20, density=True)
plt.title(title, wrap=True)
plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.savefig(pdf_path)
4 changes: 3 additions & 1 deletion pyprophet/stats.py
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Expand Up @@ -11,6 +11,7 @@

from .optimized import (find_nearest_matches as _find_nearest_matches,
count_num_positives, single_chromatogram_hypothesis_fast)
from .report import plot_hist
from statsmodels.nonparametric.kde import KDEUnivariate
from collections import namedtuple
# from .config import CONFIG
Expand Down Expand Up @@ -224,7 +225,8 @@ def pi0est(p_values, lambda_ = np.arange(0.05,1.0,0.05), pi0_method = "smoother"
else:
raise click.ClickException("pi0_method must be one of 'smoother' or 'bootstrap'.")
if (pi0<=0):
raise click.ClickException("The estimated pi0 <= 0. Check that you have valid p-values or use a different range of lambda.")
plot_hist(p, f"p-value density histogram used during pi0 estimation", "p-value", "density histogram", "pi0_estimation_error_pvalue_histogram_plot.pdf")
raise click.ClickException(f"The estimated pi0 <= 0. Check that you have valid p-values or use a different range of lambda. Current lambda range: {lambda_}")

return {'pi0': pi0, 'pi0_lambda': pi0_lambda, 'lambda_': lambda_, 'pi0_smooth': pi0Smooth}

Expand Down