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Adds pvalue return to the pp plot generation script

Merged Gregory Ashton requested to merge add-pvalue-return-to-pp-plot into master
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@@ -1350,8 +1350,9 @@ 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()
@@ -1400,9 +1401,13 @@ 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):
Loading