#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Plotting utilities, leveraging Matplotlib.
"""
__all__ = ['set_style','closefig', 'savefig']
import matplotlib.pyplot as plt
import pathlib
import matplotlib as mpl
def scatter_xy(x,y,c=None, figsize=None, xlabel=None, ylabel=None, title=None,
xlim=None, ylim=None, savefig_settings=None, ax=None,
legend=True, plot_kwargs=None, lgd_kwargs=None):
"""
Make scatter plot.
Parameters
----------
x : numpy.array
x value
y : numpy.array
y value
c : TYPE, optional
DESCRIPTION. The default is None.
figsize : list, optional
A list of two integers indicating the dimension of the figure. The default is None.
xlabel : str, optional
x-axis label. The default is None.
ylabel : str, optional
y-axis label. The default is None.
title : str, optional
Title for the plot. The default is None.
xlim : list, optional
Limits for the x-axis. The default is None.
ylim : list, optional
Limits for the y-axis. The default is None.
savefig_settings : dict, optional
the dictionary of arguments for plt.savefig(); some notes below:
- "path" must be specified; it can be any existed or non-existed path,
with or without a suffix; if the suffix is not given in "path", it will follow "format"
- "format" can be one of {"pdf", "eps", "png", "ps"}
The default is None.
ax : pyplot.axis, optional
The axis object. The default is None.
legend : bool, optional
Whether to include a legend. The default is True.
plot_kwargs : dict, optional
the keyword arguments for ax.plot(). The default is None.
lgd_kwargs : dict, optional
the keyword arguments for ax.legend(). The default is None.
Returns
-------
ax : the pyplot.axis object
"""
savefig_settings = {} if savefig_settings is None else savefig_settings.copy()
plot_kwargs = {} if plot_kwargs is None else plot_kwargs.copy()
lgd_kwargs = {} if lgd_kwargs is None else lgd_kwargs.copy()
if ax is None:
fig, ax = plt.subplots(figsize=figsize)
ax.scatter(x, y, c=c, **plot_kwargs)
if xlabel is not None:
ax.set_xlabel(xlabel)
if ylabel is not None:
ax.set_ylabel(ylabel)
if title is not None:
ax.set_title(title)
if xlim is not None:
ax.set_xlim(xlim)
if ylim is not None:
ax.set_ylim(ylim)
if legend:
ax.legend(**lgd_kwargs)
else:
ax.legend().remove()
if 'fig' in locals():
if 'path' in savefig_settings:
savefig(fig, settings=savefig_settings)
return fig, ax
else:
return ax
def plot_scatter_xy(x1,y1,x2,y2, figsize=None, xlabel=None,
ylabel=None, title=None, xlim=None, ylim=None,
savefig_settings=None, ax=None, legend=True,
plot_kwargs=None, lgd_kwargs=None):
''' Plot a scatter on top of a line plot.
Parameters
----------
x1 : array
x axis of timeseries1 - plotted as a line
y1 : array
values of timeseries1 - plotted as a line
x2 : array
x axis of scatter points
y2 : array
y of scatter points
figsize : list
a list of two integers indicating the figure size
xlabel : str
label for x-axis
ylabel : str
label for y-axis
title : str
the title for the figure
xlim : list
set the limits of the x axis
ylim : list
set the limits of the y axis
ax : pyplot.axis
the pyplot.axis object
legend : bool
plot legend or not
lgd_kwargs : dict
the keyword arguments for ax.legend()
plot_kwargs : dict
the keyword arguments for ax.plot()
savefig_settings : dict
the dictionary of arguments for plt.savefig(); some notes below:
- "path" must be specified; it can be any existed or non-existed path,
with or without a suffix; if the suffix is not given in "path", it will follow "format"
- "format" can be one of {"pdf", "eps", "png", "ps"}
Returns
-------
ax : the pyplot.axis object
See also
--------
pyleoclim.utils.plotting.set_style : set different styles for the figures. Should be set before invoking the plotting functions
pyleoclim.utils.plotting.savefig : save figures
'''
# handle dict defaults
savefig_settings = {} if savefig_settings is None else savefig_settings.copy()
plot_kwargs = {} if plot_kwargs is None else plot_kwargs.copy()
lgd_kwargs = {} if lgd_kwargs is None else lgd_kwargs.copy()
if ax is None:
fig, ax = plt.subplots(figsize=figsize)
ax.plot(x1, y1, **plot_kwargs, color='green')
ax.scatter(x2, y2, color='red')
if xlabel is not None:
ax.set_xlabel(xlabel)
if ylabel is not None:
ax.set_ylabel(ylabel)
if title is not None:
ax.set_title(title)
if xlim is not None:
ax.set_xlim(xlim)
if ylim is not None:
ax.set_ylim(ylim)
if legend:
ax.legend(**lgd_kwargs)
else:
ax.legend().remove()
if 'fig' in locals():
if 'path' in savefig_settings:
savefig(fig, settings=savefig_settings)
return fig, ax
else:
return ax
def plot_xy(x, y, figsize=None, xlabel=None, ylabel=None, title=None,
xlim=None, ylim=None,savefig_settings=None, ax=None,
legend=True, plot_kwargs=None, lgd_kwargs=None,
invert_xaxis=False, invert_yaxis=False):
''' Plot a timeseries
Parameters
----------
x : array
The time axis for the timeseries
y : array
The values of the timeseries
figsize : list
a list of two integers indicating the figure size
xlabel : str
label for x-axis
ylabel : str
label for y-axis
title : str
the title for the figure
xlim : list
set the limits of the x axis
ylim : list
set the limits of the y axis
ax : pyplot.axis
the pyplot.axis object
legend : bool
plot legend or not
lgd_kwargs : dict
the keyword arguments for ax.legend()
plot_kwargs : dict
the keyword arguments for ax.plot()
mute : bool
if True, the plot will not show;
recommend to turn on when more modifications are going to be made on ax
(going to be deprecated)
savefig_settings : dict
the dictionary of arguments for plt.savefig(); some notes below:
- "path" must be specified; it can be any existed or non-existed path,
with or without a suffix; if the suffix is not given in "path", it will follow "format"
- "format" can be one of {"pdf", "eps", "png", "ps"}
invert_xaxis : bool, optional
if True, the x-axis of the plot will be inverted
invert_yaxis : bool, optional
if True, the y-axis of the plot will be inverted
Returns
-------
ax : the pyplot.axis object
See Also
--------
pyleoclim.utils.plotting.set_style : set different styles for the figures. Should be set before invoking the plotting functions
pyleoclim.utils.plotting.savefig : save figures
'''
# handle dict defaults
savefig_settings = {} if savefig_settings is None else savefig_settings.copy()
plot_kwargs = {} if plot_kwargs is None else plot_kwargs.copy()
lgd_kwargs = {} if lgd_kwargs is None else lgd_kwargs.copy()
if ax is None:
fig, ax = plt.subplots(figsize=figsize)
ax.plot(x, y, **plot_kwargs)
if xlabel is not None:
ax.set_xlabel(xlabel)
if ylabel is not None:
ax.set_ylabel(ylabel)
if title is not None:
ax.set_title(title)
# TODO replace with ax.set_title(title, fontweight='bold') when all relevant plots use plot_xy
if xlim is not None:
ax.set_xlim(xlim)
if ylim is not None:
ax.set_ylim(ylim)
if legend:
ax.legend(**lgd_kwargs)
else:
ax.legend().remove()
if invert_xaxis:
ax.invert_xaxis()
if invert_yaxis:
ax.invert_yaxis()
if 'fig' in locals():
if 'path' in savefig_settings:
savefig(fig, settings=savefig_settings)
return fig, ax
else:
return ax
[docs]def closefig(fig=None):
'''Close the figure
Parameters
----------
fig : matplotlib.pyplot.figure
The matplotlib figure object
'''
if fig is not None:
plt.close(fig)
else:
plt.close()
[docs]def savefig(fig, path=None, dpi=300, settings={}, verbose=True):
''' Save a figure to a path
Parameters
----------
fig : matplotlib.pyplot.figure
the figure to save
path : str
the path to save the figure, can be ignored and specify in "settings" instead
dpi : int
resolution in dot (pixels) per inch. Default: 300.
settings : dict
the dictionary of arguments for plt.savefig(); some notes below:
- "path" must be specified in settings if not assigned with the keyword argument;
it can be any existed or non-existed path, with or without a suffix;
if the suffix is not given in "path", it will follow "format"
- "format" can be one of {"pdf", "eps", "png", "ps"}
verbose : bool, {True,False}
If True, print the path of the saved file.
'''
if path is None and 'path' not in settings:
raise ValueError('"path" must be specified, either with the keyword argument or be specified in `settings`!')
savefig_args = {'bbox_inches': 'tight', 'path': path, 'dpi': dpi}
savefig_args.update(settings)
path = pathlib.Path(savefig_args['path'])
savefig_args.pop('path')
dirpath = path.parent
if not dirpath.exists():
dirpath.mkdir(parents=True, exist_ok=True)
if verbose:
print(f'Directory created at: "{dirpath}"')
path_str = str(path)
if path.suffix not in ['.eps', '.pdf', '.png', '.ps']:
path = pathlib.Path(f'{path_str}.pdf')
fig.savefig(path_str, **savefig_args)
plt.close(fig)
if verbose:
print(f'Figure saved at: "{str(path)}"')
[docs]def set_style(style='journal', font_scale=1.0, dpi=300):
''' Modify the visualization style
This function is inspired by [Seaborn](https://github.com/mwaskom/seaborn).
Parameters
----------
style : {journal,web,matplotlib,_spines, _nospines,_grid,_nogrid}
set the styles for the figure:
- journal (default): fonts appropriate for paper
- web: web-like font (e.g. ggplot)
- matplotlib: the original matplotlib style
In addition, the following options are available:
- _spines/_nospines: allow to show/hide spines
- _grid/_nogrid: allow to show gridlines (default: _grid)
font_scale : float
Default is 1. Corresponding to 12 Font Size.
'''
font_dict = {
'font.size': 12,
'axes.labelsize': 12,
'axes.titlesize': 14,
'xtick.labelsize': 11,
'ytick.labelsize': 11,
'legend.fontsize': 11,
}
style_dict = {}
if 'journal' in style:
style_dict.update({
'axes.axisbelow': True,
'axes.facecolor': 'white',
'axes.edgecolor': 'black',
'axes.grid': True,
'grid.color': 'lightgrey',
'grid.linestyle': '--',
'xtick.direction': 'out',
'ytick.direction': 'out',
'font.sans-serif': ['Arial', 'DejaVu Sans', 'Liberation Sans', 'Bitstream Vera Sans', 'sans-serif'],
'axes.spines.left': True,
'axes.spines.bottom': True,
'axes.spines.right': False,
'axes.spines.top': False,
'legend.frameon': False,
'axes.linewidth': 1,
'grid.linewidth': 1,
'lines.linewidth': 2,
'lines.markersize': 6,
'patch.linewidth': 1,
'xtick.major.width': 1.25,
'ytick.major.width': 1.25,
'xtick.minor.width': 0,
'ytick.minor.width': 0,
})
elif 'web' in style:
style_dict.update({
'figure.facecolor': 'white',
'axes.axisbelow': True,
'axes.facecolor': 'whitesmoke',
'axes.edgecolor': 'lightgrey',
'axes.grid': True,
'grid.color': 'white',
'grid.linestyle': '-',
'xtick.direction': 'out',
'ytick.direction': 'out',
'text.color': 'grey',
'axes.labelcolor': 'grey',
'xtick.color': 'grey',
'ytick.color': 'grey',
'font.sans-serif': ['Arial', 'DejaVu Sans', 'Liberation Sans', 'Bitstream Vera Sans', 'sans-serif'],
'axes.spines.left': False,
'axes.spines.bottom': False,
'axes.spines.right': False,
'axes.spines.top': False,
'legend.frameon': False,
'axes.linewidth': 1,
'grid.linewidth': 1,
'lines.linewidth': 2,
'lines.markersize': 6,
'patch.linewidth': 1,
'xtick.major.width': 1.25,
'ytick.major.width': 1.25,
'xtick.minor.width': 0,
'ytick.minor.width': 0,
})
else:
raise ValueError(f'Style [{style}] not availabel!')
if '_spines' in style:
style_dict.update({
'axes.spines.left': True,
'axes.spines.bottom': True,
'axes.spines.right': True,
'axes.spines.top': True,
})
elif '_nospines' in style:
style_dict.update({
'axes.spines.left': False,
'axes.spines.bottom': False,
'axes.spines.right': False,
'axes.spines.top': False,
})
if '_grid' in style:
style_dict.update({
'axes.grid': True,
})
elif '_nogrid' in style:
style_dict.update({
'axes.grid': False,
})
figure_dict = {
'savefig.dpi': dpi,
}
# modify font size based on font scale
font_dict.update({k: v * font_scale for k, v in font_dict.items()})
for d in [style_dict, font_dict, figure_dict]:
mpl.rcParams.update(d)