#!/usr/bin/env python3
import matplotlib.pyplot as plt
import numpy as np
from postprocessor.routines.plottingabc import BasePlotter
class _MeanPlotter(BasePlotter):
"""Draw mean time series plus standard error."""
def __init__(
self,
trace_df,
trace_name,
unit_scaling,
label,
mean_color,
error_color,
mean_linestyle,
mean_marker,
xlabel,
ylabel,
plot_title,
):
super().__init__(trace_name, unit_scaling, xlabel, plot_title)
# Define attributes from arguments
self.trace_df = trace_df
self.label = label
self.mean_color = mean_color
self.error_color = error_color
self.mean_linestyle = mean_linestyle
self.mean_marker = mean_marker
# Define some labels
self.ylabel = ylabel
# Mean and standard error
self.trace_time = (
np.array(self.trace_df.columns, dtype=float) * self.unit_scaling
)
self.mean_ts = self.trace_df.mean(axis=0)
self.stderr = self.trace_df.std(axis=0) / np.sqrt(len(self.trace_df))
def plot(self, ax):
"""Draw lines and shading on provided Axes."""
super().plot(ax)
ax.plot(
self.trace_time,
self.mean_ts,
color=self.mean_color,
alpha=0.75,
linestyle=self.mean_linestyle,
marker=self.mean_marker,
label="Mean, " + self.label,
)
ax.fill_between(
self.trace_time,
self.mean_ts - self.stderr,
self.mean_ts + self.stderr,
color=self.error_color,
alpha=0.5,
label="Standard error, " + self.label,
)
ax.legend(loc="upper right")
[docs]def mean_plot(
trace_df,
trace_name="flavin",
unit_scaling=1,
label="wild type",
mean_color="b",
error_color="lightblue",
mean_linestyle="-",
mean_marker="",
xlabel="Time (min)",
ylabel="Normalised flavin fluorescence (AU)",
plot_title="",
ax=None,
):
"""Plot mean time series of a DataFrame, with standard error shading.
Parameters
----------
trace_df : pandas.DataFrame
Time series of traces (rows = cells, columns = time points).
trace_name : string
Name of trace being plotted, e.g. 'flavin'.
unit_scaling : int or float
Unit scaling factor, e.g. 1/60 to convert minutes to hours.
label : string
Name of group being plotted, e.g. a strain name.
mean_color : string
matplotlib colour string for the mean trace.
error_color : string
matplotlib colour string for the standard error shading.
mean_linestyle : string
matplotlib linestyle argument for the mean trace.
mean_marker : string
matplotlib marker argument for the mean trace.
xlabel : string
x axis label.
ylabel : string
y axis label.
plot_title : string
Plot title.
ax : matplotlib Axes
Axes in which to draw the plot, otherwise use the currently active Axes.
Examples
--------
FIXME: Add docs.
"""
plotter = _MeanPlotter(
trace_df,
trace_name,
unit_scaling,
label,
mean_color,
error_color,
mean_linestyle,
mean_marker,
xlabel,
ylabel,
plot_title,
)
if ax is None:
ax = plt.gca()
plotter.plot(ax)
return ax