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Add a parameter to name kink image in thresh_peaks #44

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Add a parameter to name kink image in thresh_peaks #44

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98d489a
Add a parameter to name kink image in thresh_peaks
julistanley Jun 18, 2022
7791014
Merge branch 'main' into julianstanley-kink_img
miraep8 Feb 24, 2023
0eba2d2
Merge branch 'main' into julianstanley-kink_img
miraep8 Feb 27, 2023
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4 changes: 2 additions & 2 deletions rendseq/make_peaks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -190,7 +190,7 @@ def _calc_thresh(z_scores, method, kink_img="./kink.png"):
return thresh


def thresh_peaks(z_scores, thresh=None, method="kink"):
def thresh_peaks(z_scores, thresh=None, method="kink", kink_image="./kink.png"):
"""Find peaks by calling z-scores above a threshold as a peak.

Parameters
Expand All @@ -202,7 +202,7 @@ def thresh_peaks(z_scores, thresh=None, method="kink"):
if none is provided. Default method is "kink"
"""
if thresh is None:
thresh = _calc_thresh(z_scores, method)
thresh = _calc_thresh(z_scores, method, kink_image)
peaks = np.zeros([len(z_scores), 2])
peaks[:, 0] = z_scores[:, 0]
peaks[:, 1] = (z_scores[:, 1] > thresh).astype(int)
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