def timeseries(X, **kwargs):
"""Plot X. See timeseries_subplot."""
pl.figure(
figsize=tuple(2 * s for s in rcParams['figure.figsize']),
subplotpars=sppars(left=0.12, right=0.98, bottom=0.13),
)
timeseries_subplot(X, **kwargs)
def timeseries(X, **kwargs):
"""
Plot X. See timeseries_subplot.
"""
pl.figure(figsize=(2 * 4, 4),
subplotpars=sppars(left=0.12, right=0.98, bottom=0.13))
timeseries_subplot(X, **kwargs)
def timeseries(X, **kwargs):
"""Plot X. See timeseries_subplot."""
pl.figure(figsize=(2*rcParams['figure.figsize'][0], rcParams['figure.figsize'][1]),
subplotpars=sppars(left=0.12, right=0.98, bottom=0.13))
timeseries_subplot(X, **kwargs)
def setup_axes(
ax=None,
panels='blue',
colorbars=[False],
right_margin=None,
left_margin=None,
projection='2d',
show_ticks=False):
"""Grid of axes for plotting, legends and colorbars.
"""
if '3d' in projection: from mpl_toolkits.mplot3d import Axes3D
avail_projections = {'2d', '3d'}
if projection not in avail_projections:
raise ValueError('choose projection from', avail_projections)
if left_margin is not None:
raise ValueError('Currently not supporting to pass `left_margin`.')
if np.any(colorbars) and right_margin is None:
right_margin = 1 - rcParams['figure.subplot.right'] + 0.21 # 0.25
elif right_margin is None:
right_margin = 1 - rcParams['figure.subplot.right'] + 0.06 # 0.10
# make a list of right margins for each panel
if not isinstance(right_margin, list):
right_margin_list = [right_margin for i in range(len(panels))]
else:
right_margin_list = right_margin
# make a figure with len(panels) panels in a row side by side
top_offset = 1 - rcParams['figure.subplot.top']
bottom_offset = 0.15 if show_ticks else 0.08
left_offset = 1 if show_ticks else 0.3 # in units of base_height
base_height = rcParams['figure.figsize'][1]
height = base_height
base_width = rcParams['figure.figsize'][0]
if show_ticks: base_width *= 1.1
draw_region_width = base_width - left_offset - top_offset - 0.5 # this is kept constant throughout
right_margin_factor = sum([1 + right_margin for right_margin in right_margin_list])
width_without_offsets = right_margin_factor * draw_region_width # this is the total width that keeps draw_region_width
right_offset = (len(panels) - 1) * left_offset
figure_width = width_without_offsets + left_offset + right_offset
draw_region_width_frac = draw_region_width / figure_width
left_offset_frac = left_offset / figure_width
right_offset_frac = 1 - (len(panels) - 1) * left_offset_frac
if ax is None:
pl.figure(figsize=(figure_width, height),
subplotpars=sppars(left=0, right=1, bottom=bottom_offset))
left_positions = [left_offset_frac, left_offset_frac + draw_region_width_frac]
for i in range(1, len(panels)):
right_margin = right_margin_list[i-1]
left_positions.append(left_positions[-1] + right_margin * draw_region_width_frac)
left_positions.append(left_positions[-1] + draw_region_width_frac)
panel_pos = [[bottom_offset], [1-top_offset], left_positions]
axs = []
if ax is None:
for icolor, color in enumerate(panels):
left = panel_pos[2][2*icolor]
bottom = panel_pos[0][0]
width = draw_region_width / figure_width
height = panel_pos[1][0] - bottom
if projection == '2d': ax = pl.axes([left, bottom, width, height])
elif projection == '3d': ax = pl.axes([left, bottom, width, height], projection='3d')
axs.append(ax)
else:
axs = ax if isinstance(ax, list) else [ax]
return axs, panel_pos, draw_region_width, figure_width
def setup_axes(
ax: Union[Axes, Sequence[Axes]] = None,
panels='blue',
colorbars=(False, ),
right_margin=None,
left_margin=None,
projection: Literal['2d', '3d'] = '2d',
show_ticks=False,
):
"""Grid of axes for plotting, legends and colorbars.
"""
make_projection_available(projection)
if left_margin is not None:
raise NotImplementedError('We currently don’t support `left_margin`.')
if np.any(colorbars) and right_margin is None:
right_margin = 1 - rcParams['figure.subplot.right'] + 0.21 # 0.25
elif right_margin is None:
right_margin = 1 - rcParams['figure.subplot.right'] + 0.06 # 0.10
# make a list of right margins for each panel
if not isinstance(right_margin, list):
right_margin_list = [right_margin for i in range(len(panels))]
else:
right_margin_list = right_margin
# make a figure with len(panels) panels in a row side by side
top_offset = 1 - rcParams['figure.subplot.top']
bottom_offset = 0.15 if show_ticks else 0.08
left_offset = 1 if show_ticks else 0.3 # in units of base_height
base_height = rcParams['figure.figsize'][1]
height = base_height
base_width = rcParams['figure.figsize'][0]
if show_ticks:
base_width *= 1.1
draw_region_width = (base_width - left_offset - top_offset - 0.5
) # this is kept constant throughout
right_margin_factor = sum(
[1 + right_margin for right_margin in right_margin_list])
width_without_offsets = (
right_margin_factor * draw_region_width
) # this is the total width that keeps draw_region_width
right_offset = (len(panels) - 1) * left_offset
figure_width = width_without_offsets + left_offset + right_offset
draw_region_width_frac = draw_region_width / figure_width
left_offset_frac = left_offset / figure_width
right_offset_frac = 1 - (len(panels) - 1) * left_offset_frac
if ax is None:
pl.figure(
figsize=(figure_width, height),
subplotpars=sppars(left=0, right=1, bottom=bottom_offset),
)
left_positions = [
left_offset_frac, left_offset_frac + draw_region_width_frac
]
for i in range(1, len(panels)):
right_margin = right_margin_list[i - 1]
left_positions.append(left_positions[-1] +
right_margin * draw_region_width_frac)
left_positions.append(left_positions[-1] + draw_region_width_frac)
panel_pos = [[bottom_offset], [1 - top_offset], left_positions]
axs = []
if ax is None:
for icolor, color in enumerate(panels):
left = panel_pos[2][2 * icolor]
bottom = panel_pos[0][0]
width = draw_region_width / figure_width
height = panel_pos[1][0] - bottom
if projection == '2d':
ax = pl.axes([left, bottom, width, height])
elif projection == '3d':
ax = pl.axes([left, bottom, width, height], projection='3d')
axs.append(ax)
else:
axs = ax if isinstance(ax, cabc.Sequence) else [ax]
return axs, panel_pos, draw_region_width, figure_width
def scatter_base(Y,
colors='blue',
highlights=[],
highlights_labels=[],
title='',
right_margin=None,
layout='2d',
titles=None,
component_name='DC',
component_indexnames=[1, 2, 3],
axlabels=None,
colorbars=[False],
sizes=[1],
cmap='viridis'):
"""
Plot scatter plot of data.
Parameters
----------
Y : np.ndarray
Data array.
layout : str
Either '2d' or '3d'.
comps : iterable
Iterable that stores the component indices.
Returns
-------
axs : matplotlib.axis or list of matplotlib.axis
Depending on whether supplying a single array or a list of arrays,
return a single axis or a list of axes.
"""
# if we have a single array, transform it into a list with a single array
avail_layouts = {'2d', '3d'}
if layout not in avail_layouts:
raise ValueError('choose layout from', avail_layouts)
if type(colors) == str:
colors = [colors]
if len(sizes) != len(colors):
if len(sizes) == 1:
sizes = [sizes[0] for i in range(len(colors))]
# try importing Axes3D
if '3d' in layout:
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import gridspec
# grid of axes for plotting and legends/colorbars
if np.any(colorbars) and right_margin is None:
right_margin = 0.25
elif right_margin is None:
right_margin = 0.01
# make a figure with panels len(colors) x 1
top_offset = 1 - rcParams['figure.subplot.top']
bottom_offset = 0.08
left_offset = 0.3 # in units of base_height
base_height = 4
height = base_height
draw_region_width = base_height - left_offset - top_offset - 0.5 # this is kept constant throughout
right_margin_factor = (1 + right_margin / (1 - right_margin))
width_without_offsets = right_margin_factor * len(
colors
) * draw_region_width # this is the total width that keeps draw_region_width
right_offset = (len(colors) - 1) * left_offset
width = width_without_offsets + left_offset + right_offset
left_offset_frac = left_offset / width
right_offset_frac = 1 - (len(colors) - 1) * left_offset_frac
figsize = (width, height)
fig = pl.figure(figsize=figsize,
subplotpars=sppars(left=0, right=1, bottom=bottom_offset))
gs = gridspec.GridSpec(nrows=1,
ncols=2 * len(colors),
width_ratios=[
r for i in range(len(colors))
for r in [1 - right_margin, right_margin]
],
left=left_offset_frac,
right=right_offset_frac,
wspace=0)
pos = gs.get_grid_positions(fig)
fig.suptitle(title)
count = 1
bool3d = True if layout == '3d' else False
axs = []
for icolor, color in enumerate(colors):
# set up panel
if layout == 'unfolded 3d' and count != 3:
ax = fig.add_subplot(2, 2, count)
bool3d = False
elif layout == 'unfolded 3d' and count == 3:
ax = fig.add_subplot(2, 2, count, projection='3d')
bool3d = True
elif layout == '2d':
ax = pl.subplot(gs[2 * (count - 1)])
elif layout == '3d':
ax = pl.subplot(gs[2 * (count - 1)], projection='3d')
if not bool3d:
data = Y[:, 0], Y[:, 1]
else:
data = Y[:, 0], Y[:, 1], Y[:, 2]
# do the plotting
if type(color) != str or color != 'white':
sct = ax.scatter(*data,
c=color,
edgecolors='face',
s=sizes[icolor],
cmap=cmap)
if colorbars[icolor]:
pos = gs.get_grid_positions(fig)
left = pos[2][2 * (count - 1) + 1]
bottom = pos[0][0]
width = 0.006 * draw_region_width
# print(0.2*(pos[3][2*(count-1)+1] - left))
height = pos[1][0] - bottom
# again shift to left
left = pos[3][2 * (count - 1)] + width
rectangle = [left, bottom, width, height]
ax_cb = fig.add_axes(rectangle)
cb = pl.colorbar(sct,
format=ticker.FuncFormatter(ticks_formatter),
cax=ax_cb)
# set the titles
if titles is not None:
ax.set_title(titles[icolor])
# output highlighted data points
for iihighlight, ihighlight in enumerate(highlights):
data = [Y[ihighlight, 0]], [Y[ihighlight, 1]]
if bool3d:
data = [Y[ihighlight, 0]], [Y[ihighlight,
1]], [Y[ihighlight, 2]]
ax.scatter(*data,
c='black',
facecolors='black',
edgecolors='black',
marker='x',
s=40,
zorder=20)
highlight = (highlights_labels[iihighlight]
if len(highlights_labels) > 0 else str(ihighlight))
# the following is a Python 2 compatibility hack
ax.text(*([d[0] for d in data] + [highlight]), zorder=20)
ax.set_xticks([])
ax.set_yticks([])
if bool3d:
ax.set_zticks([])
# scale limits to match data
ax.autoscale_view()
axs.append(ax)
count += 1
# set default axlabels
if axlabels is None:
if layout == '2d':
axlabels = [[
component_name + str(i) for i in idcs
] for idcs in [component_indexnames for iax in range(len(axs))]]
elif layout == '3d':
axlabels = [[
component_name + str(i) for i in idcs
] for idcs in [component_indexnames for iax in range(len(axs))]]
elif layout == 'unfolded 3d':
axlabels = [[
component_name + str(component_indexnames[i - 1]) for i in idcs
] for idcs in [[2, 3], [1, 2], [1, 2, 3], [1, 3]]]
# set axlabels
bool3d = True if layout == '3d' else False
for iax, ax in enumerate(axs):
if layout == 'unfolded 3d' and iax != 2:
bool3d = False
elif layout == 'unfolded 3d' and iax == 2:
bool3d = True
if axlabels is not None:
ax.set_xlabel(axlabels[iax][0])
ax.set_ylabel(axlabels[iax][1])
if bool3d:
# shift the label closer to the axis
ax.set_zlabel(axlabels[iax][2], labelpad=-7)
return axs
