From 551acc7431866d260aa901be1490df9a1cc79b4d Mon Sep 17 00:00:00 2001
From: Peter Swain <pswain@Home-iMac.local>
Date: Tue, 21 May 2024 10:25:31 +0100
Subject: [PATCH] feature(bud_to_bud_plot): more than one bud event
---
src/wela/plotting.py | 61 ++++++++++++++++++++++++++++++++------------
1 file changed, 44 insertions(+), 17 deletions(-)
diff --git a/src/wela/plotting.py b/src/wela/plotting.py
index 39ce895..8595309 100644
--- a/src/wela/plotting.py
+++ b/src/wela/plotting.py
@@ -610,6 +610,7 @@ def bud_to_bud_plot(
colour="b",
group=None,
nbins=None,
+ no_future_buddings=2,
return_signal=False,
df=None,
title=None,
@@ -636,9 +637,11 @@ def bud_to_bud_plot(
Colour of lines.
group: str, optional
The name of the group to plot.
- nbins: integer, optional
+ nbins: int, optional
The number of time bins to partition the interval between the
first and the second budding event.
+ no_future_buddings: int, optional
+ The number of future budding events to include. Default is 1.
return_signal: boolean, optional
If True, return the signal for each cell interpolated to the time
bins.
@@ -673,29 +676,24 @@ def bud_to_bud_plot(
t = t / 60
tpt_i = np.argmin((t - tpt) ** 2)
# get data for bud-to-bud around tpt for each cell
- local_signals, local_times = [], []
- for i in range(signal_data.shape[0]):
- future_buddings = np.nonzero(buddings[i, :][tpt_i:])[0]
- if np.any(future_buddings):
- end_tpt_i = tpt_i + future_buddings[0]
- past_buddings = np.nonzero(buddings[i, :][:tpt_i])[0]
- if np.any(past_buddings):
- start_tpt_i = past_buddings[-1]
- local_data = signal_data[i, start_tpt_i : end_tpt_i + 1]
- if ~np.all(np.isnan(local_data)):
- local_signals.append(local_data)
- local_times.append(t[start_tpt_i : end_tpt_i + 1])
+ local_signals, local_times = get_bud_to_bud_data(
+ tpt_i,
+ t,
+ signal_data,
+ buddings,
+ no_future_buddings_index=no_future_buddings - 1,
+ )
if local_times:
- # find bins for normalised time, between 0 and 1
+ # find bins for normalised time, between 0 and no_future_buddings
nbins = int(np.median([len(local_time) for local_time in local_times]))
- ntbins = np.linspace(0, 1, nbins)
+ ntbins = np.linspace(0, no_future_buddings, nbins)
# interpolate each local signal to make a new signal
new_signal = np.nan * np.ones((len(local_signals), nbins))
for i in range(len(local_signals)):
s = local_signals[i]
- # normalise time between 0 and 1
+ # normalise time between 0 and no_future_buddings
nt = local_times[i] - local_times[i][0]
- nt /= nt[-1]
+ nt = nt / nt[-1] * no_future_buddings
# interpolate into the bins
new_signal[i, :] = np.interp(
ntbins,
@@ -727,3 +725,32 @@ def bud_to_bud_plot(
plt.show(block=False)
if return_signal:
return new_signal
+
+
+def get_bud_to_bud_data(
+ tpt_i, t, signal_data, buddings, no_future_buddings_index=0
+):
+ """
+ Get data for bud-to-bud around tpt for each cell.
+
+ Parameters
+ ----------
+ no_future_buddings_index: int
+ The index to select future buddings, with 0 representing the next
+ budding event.
+ """
+ local_signals, local_times = [], []
+ for i in range(signal_data.shape[0]):
+ future_buddings = np.nonzero(buddings[i, :][tpt_i:])[0]
+ if np.any(future_buddings) and (
+ future_buddings.size > no_future_buddings_index
+ ):
+ end_tpt_i = tpt_i + future_buddings[no_future_buddings_index]
+ past_buddings = np.nonzero(buddings[i, :][:tpt_i])[0]
+ if np.any(past_buddings):
+ start_tpt_i = past_buddings[-1]
+ local_data = signal_data[i, start_tpt_i : end_tpt_i + 1]
+ if ~np.all(np.isnan(local_data)):
+ local_signals.append(local_data)
+ local_times.append(t[start_tpt_i : end_tpt_i + 1])
+ return local_signals, local_times
--
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