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Commit 0c677ec9 authored by Gregory Ashton's avatar Gregory Ashton
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Adds pvalue return to the pp plot generation script

Useful if the pvalues needs to be logged elsewhere from a script
parent 5ae5e02a
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......@@ -1469,8 +1469,9 @@ def make_pp_plot(results, filename=None, save=True, confidence_interval=0.9,
Returns
-------
fig:
matplotlib figure
fig, pvals:
matplotlib figure and a NamedTuple with attributes `combined_pvalue`,
`pvalues`, and `names`.
"""
credible_levels = pd.DataFrame()
......@@ -1519,9 +1520,13 @@ def make_pp_plot(results, filename=None, save=True, confidence_interval=0.9,
filename = 'outdir/pp.png'
fig.savefig(filename, dpi=500)
Pvals = namedtuple('pvals', ['combined_pvalue', 'pvalues', 'names'])
pvals = Pvals(combined_pvalue=scipy.stats.combine_pvalues(pvalues)[1],
pvalues=pvalues,
names=list(credible_levels.keys()))
logger.info(
"Combined p-value: {}".format(scipy.stats.combine_pvalues(pvalues)[1]))
return fig
"Combined p-value: {}".format(pvals.combined_pvalue))
return fig, pvals
class ResultError(Exception):
......
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