From e926896312e73f67609b4e3077e343f060cd4006 Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 16 May 2024 17:06:48 +0100
Subject: [PATCH] feature(kymograph): added buddings, scale, robust
Using Arin's code.
Renamed directories to include Arin's name.
---
.../align.py | 0
.../autoreg.py | 0
.../crosscorr.py | 0
.../fft.py | 0
.../fft_function.py | 0
.../findpeaks.py | 0
.../standardscaler.py | 0
.../__init__.py | 0
.../boxplot.py | 0
.../heatmap.py | 0
.../histogram.py | 0
.../mean_plot.py | 0
.../median_plot.py | 0
.../plot_utils.py | 0
.../plottingabc.py | 0
.../single_birth_plot.py | 0
.../single_plot.py | 0
src/wela/dataloader.py | 2 +-
src/wela/imageviewer.py | 26 +++----
src/wela/plotting.py | 72 +++++++++++++++++--
20 files changed, 79 insertions(+), 21 deletions(-)
rename limbo/{old_data_analysis => arin_data_analysis}/align.py (100%)
rename limbo/{old_data_analysis => arin_data_analysis}/autoreg.py (100%)
rename limbo/{old_data_analysis => arin_data_analysis}/crosscorr.py (100%)
rename limbo/{old_data_analysis => arin_data_analysis}/fft.py (100%)
rename limbo/{old_data_analysis => arin_data_analysis}/fft_function.py (100%)
rename limbo/{old_data_analysis => arin_data_analysis}/findpeaks.py (100%)
rename limbo/{old_data_analysis => arin_data_analysis}/standardscaler.py (100%)
rename limbo/{old_plotting => arin_plotting}/__init__.py (100%)
rename limbo/{old_plotting => arin_plotting}/boxplot.py (100%)
rename limbo/{old_plotting => arin_plotting}/heatmap.py (100%)
rename limbo/{old_plotting => arin_plotting}/histogram.py (100%)
rename limbo/{old_plotting => arin_plotting}/mean_plot.py (100%)
rename limbo/{old_plotting => arin_plotting}/median_plot.py (100%)
rename limbo/{old_plotting => arin_plotting}/plot_utils.py (100%)
rename limbo/{old_plotting => arin_plotting}/plottingabc.py (100%)
rename limbo/{old_plotting => arin_plotting}/single_birth_plot.py (100%)
rename limbo/{old_plotting => arin_plotting}/single_plot.py (100%)
diff --git a/limbo/old_data_analysis/align.py b/limbo/arin_data_analysis/align.py
similarity index 100%
rename from limbo/old_data_analysis/align.py
rename to limbo/arin_data_analysis/align.py
diff --git a/limbo/old_data_analysis/autoreg.py b/limbo/arin_data_analysis/autoreg.py
similarity index 100%
rename from limbo/old_data_analysis/autoreg.py
rename to limbo/arin_data_analysis/autoreg.py
diff --git a/limbo/old_data_analysis/crosscorr.py b/limbo/arin_data_analysis/crosscorr.py
similarity index 100%
rename from limbo/old_data_analysis/crosscorr.py
rename to limbo/arin_data_analysis/crosscorr.py
diff --git a/limbo/old_data_analysis/fft.py b/limbo/arin_data_analysis/fft.py
similarity index 100%
rename from limbo/old_data_analysis/fft.py
rename to limbo/arin_data_analysis/fft.py
diff --git a/limbo/old_data_analysis/fft_function.py b/limbo/arin_data_analysis/fft_function.py
similarity index 100%
rename from limbo/old_data_analysis/fft_function.py
rename to limbo/arin_data_analysis/fft_function.py
diff --git a/limbo/old_data_analysis/findpeaks.py b/limbo/arin_data_analysis/findpeaks.py
similarity index 100%
rename from limbo/old_data_analysis/findpeaks.py
rename to limbo/arin_data_analysis/findpeaks.py
diff --git a/limbo/old_data_analysis/standardscaler.py b/limbo/arin_data_analysis/standardscaler.py
similarity index 100%
rename from limbo/old_data_analysis/standardscaler.py
rename to limbo/arin_data_analysis/standardscaler.py
diff --git a/limbo/old_plotting/__init__.py b/limbo/arin_plotting/__init__.py
similarity index 100%
rename from limbo/old_plotting/__init__.py
rename to limbo/arin_plotting/__init__.py
diff --git a/limbo/old_plotting/boxplot.py b/limbo/arin_plotting/boxplot.py
similarity index 100%
rename from limbo/old_plotting/boxplot.py
rename to limbo/arin_plotting/boxplot.py
diff --git a/limbo/old_plotting/heatmap.py b/limbo/arin_plotting/heatmap.py
similarity index 100%
rename from limbo/old_plotting/heatmap.py
rename to limbo/arin_plotting/heatmap.py
diff --git a/limbo/old_plotting/histogram.py b/limbo/arin_plotting/histogram.py
similarity index 100%
rename from limbo/old_plotting/histogram.py
rename to limbo/arin_plotting/histogram.py
diff --git a/limbo/old_plotting/mean_plot.py b/limbo/arin_plotting/mean_plot.py
similarity index 100%
rename from limbo/old_plotting/mean_plot.py
rename to limbo/arin_plotting/mean_plot.py
diff --git a/limbo/old_plotting/median_plot.py b/limbo/arin_plotting/median_plot.py
similarity index 100%
rename from limbo/old_plotting/median_plot.py
rename to limbo/arin_plotting/median_plot.py
diff --git a/limbo/old_plotting/plot_utils.py b/limbo/arin_plotting/plot_utils.py
similarity index 100%
rename from limbo/old_plotting/plot_utils.py
rename to limbo/arin_plotting/plot_utils.py
diff --git a/limbo/old_plotting/plottingabc.py b/limbo/arin_plotting/plottingabc.py
similarity index 100%
rename from limbo/old_plotting/plottingabc.py
rename to limbo/arin_plotting/plottingabc.py
diff --git a/limbo/old_plotting/single_birth_plot.py b/limbo/arin_plotting/single_birth_plot.py
similarity index 100%
rename from limbo/old_plotting/single_birth_plot.py
rename to limbo/arin_plotting/single_birth_plot.py
diff --git a/limbo/old_plotting/single_plot.py b/limbo/arin_plotting/single_plot.py
similarity index 100%
rename from limbo/old_plotting/single_plot.py
rename to limbo/arin_plotting/single_plot.py
diff --git a/src/wela/dataloader.py b/src/wela/dataloader.py
index 98a11a0..6ca43fc 100644
--- a/src/wela/dataloader.py
+++ b/src/wela/dataloader.py
@@ -10,7 +10,7 @@ try:
from postprocessor.grouper import Grouper
from wela.add_bud_fluorescence import add_bud_fluorescence
except ModuleNotFoundError:
- print("Can only load tsv files - cannot find postprocessor.")
+ print("Can only load tsv files - cannot find aliby's postprocessor.")
class dataloader:
diff --git a/src/wela/imageviewer.py b/src/wela/imageviewer.py
index 3b7fd87..ff3c762 100644
--- a/src/wela/imageviewer.py
+++ b/src/wela/imageviewer.py
@@ -9,6 +9,7 @@ from agora.io.cells import Cells
from agora.io.metadata import parse_metadata
from aliby.io.image import dispatch_image
from aliby.tile.tiler import Tiler
+from aliby.io.omero import UnsafeImage as OImage
def colormap(channel):
@@ -206,25 +207,18 @@ class LocalImageViewer(BaseImageViewer):
class RemoteImageViewer(BaseImageViewer):
"""Fetching remote images with tiling and outline display."""
- credentials = ("host", "username", "password")
-
- def __init__(self, h5file: str, server_info: t.Dict[str, str]):
+ def __init__(
+ self, h5file: str, server_info: t.Dict[str, str], omero_id: int
+ ):
"""Initialise using a h5file and importing aliby.io.omero."""
- from aliby.io.omero import UnsafeImage as OImage
-
h5file_path = Path(h5file)
super().__init__(h5file_path)
- server_info = server_info or {
- k: self.attrs["parameters"]["general"][k] for k in self.credentials
- }
- logfiles_meta = parse_metadata(h5file_path.parent)
- image_id = logfiles_meta.get("image_id")
- if image_id is None:
- with h5py.File(h5file_path, "r") as f:
- image_id = f.attrs.get("image_id")
- if image_id is None:
- raise ("No valid image_id found in metadata.")
- image = OImage(image_id, **server_info)
+ with h5py.File(h5file_path, "r") as f:
+ breakpoint()
+ self.image_id = f.attrs.get("image_id")
+
+ image = OImage(omero_id, **server_info)
+ breakpoint()
self.tiler = Tiler.from_h5(image, h5file_path)
self.cells = Cells.from_source(h5file_path)
diff --git a/src/wela/plotting.py b/src/wela/plotting.py
index 961ad11..025e518 100644
--- a/src/wela/plotting.py
+++ b/src/wela/plotting.py
@@ -5,18 +5,28 @@ import matplotlib.pylab as plt
import numpy as np
import numpy.matlib
+try:
+ from sklearn.preprocessing import StandardScaler
+except ModuleNotFoundError:
+ pass
+
def kymograph(
df,
hue="median_GFP",
x="time",
y="id",
+ group=None,
xtick_step_in_hours=5,
vmax=None,
vmin=None,
cmap=None,
+ buddings=True,
figsize=(6, 10),
title=None,
+ filterfunc=None,
+ standardscale=False,
+ robust=False,
returnfig=False,
):
"""
@@ -26,12 +36,47 @@ def kymograph(
Time is assumed to be in hours.
+ Arguments
+ ---------
+ df: pd.DataFrame
+ Dataframe of data to plot.
+ hue: string
+ Variable to plot using colour.
+ x: string, optional
+ Variable for x-axis.
+ y: string, optional
+ Variable for y-axis:
+ group: string, optional
+ Group, or strain, to plot.
+ xtick_step_in_hours: int, optional
+ Set the interval between ticks on the x-axis.
+ vmax, vmin: float, optional
+ Define the data range covered by the colormap.
+ cmap: matplotlib.cm colormap, optional
+ The colourmap to use.
+ buddings: boolean, optional
+ If True, show budding events as black dots.
+ figsize: (int, int)
+ The size of the figure.
+ title: string, optional
+ Title ot use.
+ filterfunc: function, optional
+ Filter to apply to the data, assuming that the time series are
+ in rows.
+ standardscale: boolean, optional
+ If True, scale the mean of each single-cell time series to zero
+ and its standard deviation to one.
+ robust: boolean, optional
+ If True, change colourmap to show 2-98% of all the data's values.
+ returnfig: boolean, optional
+ If True, return fig and ax.
+
Examples
--------
>>> from wela.plotting import kymograph
>>> kymograph(dl.df, hue="median_GFP")
>>> kymograph(dl.df, hue="bud_volume", title="2% Gal")
- >>> kymograph(dl.df, hue="buddings")
+ >>> kymograph(dl.df, hue="buddings", group="Msn2")
"""
if cmap is None:
if hue == "buddings":
@@ -46,10 +91,25 @@ def kymograph(
cmap = matplotlib.cm.Spectral
else:
cmap = matplotlib.cm.viridis
+ if group is not None:
+ df = df[df.group == group]
wdf = df.pivot(index=y, columns=x, values=hue)
dt = np.min(np.diff(np.sort(df.time.unique())))
- # from Arin
data = wdf.to_numpy()
+ if filterfunc is not None:
+ data = filterfunc(data)
+ if standardscale:
+ scaler = StandardScaler().fit(data.transpose())
+ data = scaler.transform(data.transpose()).transpose()
+ if robust:
+ vmin = np.nanpercentile(data, 2)
+ vmax = np.nanpercentile(data, 98)
+ # make axes even
+ if standardscale:
+ if np.abs(vmin) > np.abs(vmax):
+ vmax = -vmin
+ else:
+ vmin = -vmax
# define horizontal axis ticks and labels
xtick_min = 0
xtick_max = dt * data.shape[1]
@@ -66,15 +126,19 @@ def kymograph(
ax.set_xlabel(x)
ax.set_ylabel(y)
ax.set_title(title)
- trace_heatmap = ax.imshow(
+ heatmap = ax.imshow(
data,
cmap=cmap,
interpolation="none",
vmax=vmax,
vmin=vmin,
)
+ if buddings:
+ buddings = df.pivot(index=y, columns=x, values="buddings").to_numpy()
+ bud_mask = np.ma.masked_where(buddings == 0, buddings)
+ ax.imshow(bud_mask, interpolation="none")
ax.figure.colorbar(
- mappable=trace_heatmap,
+ mappable=heatmap,
ax=ax,
label=hue,
aspect=50,
--
GitLab