From 68d4b0eeac31cd5a4d92e6d67e69a23b2ed370ee Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 16 May 2024 22:01:08 +0100
Subject: [PATCH] added sorting
---
src/wela/dataloader.py | 9 ++++++---
src/wela/plotting.py | 14 +++++++++++++-
2 files changed, 19 insertions(+), 4 deletions(-)
diff --git a/src/wela/dataloader.py b/src/wela/dataloader.py
index 6ca43fc..f19a8e0 100644
--- a/src/wela/dataloader.py
+++ b/src/wela/dataloader.py
@@ -651,9 +651,12 @@ class dataloader:
print(group, "not recognised")
return None, None
else:
- wdf = df[df.group == group].pivot(
- columns="time", index="id", values=signal
- )
+ if group is None:
+ wdf = df.pivot(columns="time", index="id", values=signal)
+ else:
+ wdf = df[df.group == group].pivot(
+ columns="time", index="id", values=signal
+ )
time = wdf.columns.to_numpy()
# each column is a time series
values = wdf.to_numpy()
diff --git a/src/wela/plotting.py b/src/wela/plotting.py
index 025e518..4e47b06 100644
--- a/src/wela/plotting.py
+++ b/src/wela/plotting.py
@@ -21,12 +21,13 @@ def kymograph(
vmax=None,
vmin=None,
cmap=None,
- buddings=True,
+ buddings=False,
figsize=(6, 10),
title=None,
filterfunc=None,
standardscale=False,
robust=False,
+ sort_order=None,
returnfig=False,
):
"""
@@ -68,6 +69,8 @@ def kymograph(
and its standard deviation to one.
robust: boolean, optional
If True, change colourmap to show 2-98% of all the data's values.
+ sort_order: np.array, optional
+ An array specifying the order to plot the cells.
returnfig: boolean, optional
If True, return fig and ax.
@@ -77,6 +80,11 @@ def kymograph(
>>> kymograph(dl.df, hue="median_GFP")
>>> kymograph(dl.df, hue="bud_volume", title="2% Gal")
>>> kymograph(dl.df, hue="buddings", group="Msn2")
+ >>>
+ >>> from wela.sorting import sort_by_budding
+ >>> _, buddings = dl.get_time_series(buddings)
+ >>> sort_order = sort_by_budding(buddings)
+ >>> kymograph(dl.df, hue="flavin", sort_order=sort_order)
"""
if cmap is None:
if hue == "buddings":
@@ -96,6 +104,8 @@ def kymograph(
wdf = df.pivot(index=y, columns=x, values=hue)
dt = np.min(np.diff(np.sort(df.time.unique())))
data = wdf.to_numpy()
+ if sort_order is not None:
+ data = data[np.argsort(sort_order), :]
if filterfunc is not None:
data = filterfunc(data)
if standardscale:
@@ -135,6 +145,8 @@ def kymograph(
)
if buddings:
buddings = df.pivot(index=y, columns=x, values="buddings").to_numpy()
+ if sort_order is not None:
+ buddings = buddings[np.argsort(sort_order), :]
bud_mask = np.ma.masked_where(buddings == 0, buddings)
ax.imshow(bud_mask, interpolation="none")
ax.figure.colorbar(
--
GitLab