# -*- coding: utf-8 -*-
"""
This module contains functionality to comfortably create plots.
"""
from math import floor, ceil, pi
from itertools import islice, chain, cycle, repeat
from collections.abc import Iterable, Mapping
from typing import Union
from warnings import warn
import pandas as pd
import pandas.api.types as pd_types
import numpy as np
from scipy import interpolate
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.colors as plt_colors
import matplotlib.cm as plt_cm
import matplotlib.lines as mlines
import mpl_toolkits.axes_grid1 as axg1
from configparser import ConfigParser
from IPython.display import HTML, display
from tabulate import tabulate
_col_labels = {
'count': 'Anzahl'
}
[docs]def spec_col_labels(**kwargs):
"""
Specify labels for column names to be automatically used in plots.
:param kwargs: A map of column names and labels.
"""
_col_labels.update(kwargs)
[docs]def spec_col_file(filename):
"""
Specify an INI file with column names to be automatically used in plots.
The column-label-pairs must be placed under the INI section `[Columns]`.
:param filename: A path to the INI file.
"""
cfg = ConfigParser()
cfg.read(filename, encoding='utf8')
_col_labels.update(cfg['Columns'])
def _col_label(label, column):
if label is not None:
return label
if column in _col_labels:
return _col_labels[column]
return column
[docs]def table(data: pd.DataFrame, columns=None, labels=None,
with_index=True, index_label=None, limit=None):
"""
Displays an HTML table with the given data.
A subset of columns can be selected with `columns`.
The labels in the header can be explicitly specified with `labels`.
Does not support multi-indexes.
Calls `IPython.display.display()` to present the HTML table.
:param data: A Pandas DataFrame
:param columns: An iterable with column names. (optional)
:param labels: An iterable with column labels. (optional)
Must be the same size as the columns.
:param with_index: A switch to include or exclude the index. (optional)
:param index_label: A string or an iterable with labels for the index.
(optional)
:param limit: A maximum number of rows to display. (optional)
"""
if data.empty:
display(HTML('<p>No Entries</p>'))
columns = columns or data.columns
if labels:
headers = labels
else:
headers = [_col_labels[c] if c in _col_labels else c for c in columns]
if with_index:
headers.insert(0, index_label or 'index')
def cells(r):
return chain((r[0],), (getattr(r, c) for c in columns))
else:
def cells(r):
return (getattr(r, c) for c in columns)
rows = map(cells, data.itertuples())
if limit:
rows = islice(rows, limit)
display(HTML(tabulate(rows, tablefmt='html', headers=headers)))
def _default_figure_handler(subplot, fig, ax=None,
title=None, pad=None,
file_name=None, file_dpi=None):
if not fig:
return
if not subplot:
if pad is not None:
fig.tight_layout(pad=pad)
if file_name:
fig.savefig(file_name, dpi=file_dpi)
if title:
ax = ax or fig.gca()
if ax:
ax.set_title(title)
if not subplot:
plt.show()
current_figure = None
current_grid = (1, 1)
_figure_handler = _default_figure_handler
def _finish_figure(fig=None, **kwargs):
if fig is None:
return
_figure_handler(subplot=_in_multiplot(), fig=fig, **kwargs)
[docs]def begin(figsize=(10, 5), grid=(1, 1)):
"""
Begins a figure with multiple subplots.
:param figsize: A tuple with the figure size in inches (width, height).
(optional)
:param grid: The grid size to place the subplots in (rows, columns).
(optional)
"""
global current_figure, current_grid
if current_figure is not None:
warn("There is already an open figure. Did you use end()?")
current_figure = plt.figure(figsize=figsize)
current_grid = grid
[docs]def end(pad=1.5, w_pad=None, h_pad=None,
file_name=None, file_dpi=300):
"""
Finalizes a figure with multiple subplots.
:param pad: Padding around the figure. (optional)
:param w_pad: Horizontal space between subplots. (optional)
See `matplotlib.pyplot.tight_layout()`.
:param h_pad: Vertical space between subplots. (optional)
See `matplotlib.pyplot.tight_layout()`.
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
global current_figure, current_title
if current_figure is None:
raise Exception("No current figure. Did you use begin()?")
if pad is not None:
plt.tight_layout(pad=pad, h_pad=h_pad, w_pad=w_pad)
elif h_pad is not None or w_pad is not None:
plt.tight_layout(h_pad=h_pad, w_pad=w_pad)
fig = current_figure
current_figure = None
_finish_figure(
fig=fig, pad=None,
file_name=file_name, file_dpi=file_dpi)
def _in_multiplot():
global current_figure
return current_figure is not None
def _plt(figsize=(10, 4), pos=(0, 0), rowspan=1, colspan=1):
global current_figure, current_grid
if current_figure:
ax = plt.subplot2grid(current_grid, pos,
rowspan=rowspan, colspan=colspan)
return (current_figure, ax)
else:
fig = plt.figure(figsize=figsize)
return (fig, plt.gca())
[docs]def subplot(pos=(0, 0), rowspan=1, colspan=1):
"""
Prepares a sub-plot inside the current figure between calls
of `begin()` and `end()`.
This method is useful, if a custom plot must be integrated
into a multiplot created with `mastersign.datasience.plot`.
:param pos: The position in the grid of a multiplot. (optional)
:param rowspan: The number of rows to span in the grid
of a multiplot. (optional)
:param colspan: The number of columns to span in the grid
of a multiplot. (optional)
:return: A tuple with Matplotlib figure and axes: ``(fig, ax)``.
"""
if not _in_multiplot():
raise Exception("No current figure. Did you use begin()?")
return _plt(pos=pos, rowspan=rowspan, colspan=colspan)
def _build_key_colors(keys, color):
if isinstance(color, str):
return repeat(color, len(keys))
elif isinstance(color, Mapping):
return [color.get(k, None) or next(plt.gca()._get_lines.prop_cycler)['color']
for k in keys]
elif isinstance(color, Iterable):
return cycle(color)
else:
return [next(plt.gca()._get_lines.prop_cycler)['color'] for k in keys]
[docs]def pie(data: Union[pd.DataFrame, pd.Series],
column=None, label_column=None,
color_column=None, color=None,
startangle=180, counterclock=False,
sort_by=None, title=None, pct=True,
figsize=(4, 4), pad=1, pos=(0, 0), rowspan=1, colspan=1,
file_name=None, file_dpi=300):
"""
Display a pie chart with values from a column in a DataFrame
or a Series.
:param data: A Pandas DataFrame or Series.
:param column: The column to use if `data` is a DataFrame.
:param label_column: A column to use for the labels. (optional)
By default the index is used.
:param color_column: A column with color names or RGB hex values.
(optional)
:param color: A list or dict for the colors in the pie.
(optional)
If it is a dict the keys are the labels.
Gets overridden by `color_column`.
:param sort_by: The sort mode `None`, `"label"`, or `"value"`
(optional)
:param startangle: The start angle in degrees. (optional)
:param counterclock: A switch to control the angular order. (optional)
:param title: The title of the plot. (optional)
:param pct: A switch to display percentages. (optional)
:param figsize: The figure size in inches. (optional)
:param pad: Padding around the figure. (optional)
:param pos: The position in the grid of a multiplot. (optional)
:param rowspan: The number of rows to span in the grid
of a multiplot. (optional)
:param colspan: The number of columns to span in the grid
of a multiplot. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
if isinstance(data, pd.DataFrame):
# data is a DataFrame
if column is None:
raise TypeError("If data is a DataFrame, column must be specified.")
if sort_by:
data = data.sort_values(by=label_column) \
if label_column else data.sort_index()
if sort_by == 'value':
data.sort_values(by=column, ascending=False, inplace=True)
x = data[column]
labels = data[label_column] if label_column else data.index
else:
# data is assumed to be a Series
if sort_by:
data = data.sort_index()
if sort_by == 'value':
data.sort_values(ascending=False, inplace=True)
x = data
labels = data.index
color_column = None # ignore color_column for Series
(fig, ax) = _plt(figsize=figsize, pos=pos,
rowspan=rowspan, colspan=colspan)
if color_column:
colors = data[color_column]
elif isinstance(color, Mapping):
colors = [color.get(l) or next(plt.gca()._get_lines.prop_cycler)['color']
for l in labels]
elif color:
colors = color
else:
colors = None
if pct:
ax.pie(x, labels=labels, colors=colors,
startangle=startangle, counterclock=counterclock,
autopct='%1.1f%%')
else:
ax.pie(x, labels=labels, colors=colors,
startangle=startangle, counterclock=counterclock)
ax.axis('equal')
_finish_figure(
fig=fig, ax=ax, title=title, pad=pad,
file_name=file_name, file_dpi=file_dpi)
[docs]def pie_groups(data: Union[pd.DataFrame, pd.Series],
column=None, sort_by=None,
startangle=180, counterclock=False,
title=None, pct=True, color=None,
figsize=(4, 4), pad=1, pos=(0, 0), rowspan=1, colspan=1,
file_name=None, file_dpi=300):
"""
Display a pie chart by counting rows according to a column value
from a DataFrame or values from a Series.
:param data: A Pandas DataFrame or Series.
:param column: The column to use for grouping.
:param sort_by: The sort mode `None`, `"label"`, or `"value"`
:param startangle: The start angle in degrees. (optional)
:param counterclock: A switch to control the angular order. (optional)
:param title: The title of the plot.
:param pct: A switch to display percentages.
:param color: A list or dict for the colors in the pie.
(optional)
If it is a dict the groups are the labels.
:param figsize: The figure size in inches. (optional)
:param pad: Padding around the figure. (optional)
:param pos: The position in the grid of a multiplot. (optional)
:param rowspan: The number of rows to span in the grid
of a multiplot. (optional)
:param colspan: The number of columns to span in the grid
of a multiplot. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
if isinstance(data, pd.DataFrame):
groups = data.groupby(column, sort=False).size()
else:
groups = data.groupby(by=data, sort=False).size()
group_data = pd.DataFrame({'value': groups}, index=groups.index)
pie(group_data, 'value', sort_by=sort_by,
startangle=startangle, counterclock=counterclock,
title=title, pct=pct, color=color,
figsize=figsize, pad=pad, pos=pos, rowspan=rowspan, colspan=colspan,
file_name=file_name, file_dpi=file_dpi)
[docs]def bar(data: Union[pd.DataFrame, pd.Series],
value_column=None, label_column=None,
color_column=None, cmap=None, color=None,
xlabel=None, ylabel=None, title=None,
figsize=(10, 4), pad=1, pos=(0, 0), rowspan=1, colspan=1,
file_name=None, file_dpi=300):
"""
Display a bar chart from columns in a DataFrame or a Series.
:param data: A Pandas DataFrame or Series.
:param value_column: The column with the values for the bars height.
:param label_column: The column with the labels for the bars. (optional)
:param color_column: The column with a numeric value for choosing
a color from a color map or strings
for explicit colors. (optional)
:param cmap: The name of a color map to use with `color_column`.
(optional)
:param color: A color for all bars or a list with colors. (optional)
`color_column` superseeds `color`.
:param xlabel: The label for the X axis. (optional)
:param ylabel: The label for the Y axis. (optional)
:param title: The title of the plot. (optional)
:param figsize: The figure size in inches. (optional)
:param pad: Padding around the figure. (optional)
:param pos: The position in the grid of a multiplot. (optional)
:param rowspan: The number of rows to span in the grid
of a multiplot. (optional)
:param colspan: The number of columns to span in the grid
of a multiplot. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
if isinstance(data, pd.DataFrame):
all_columns = [value_column, label_column, color_column]
columns = set(c for c in all_columns if c)
data = data.loc[:, columns].dropna()
values = data[value_column]
if label_column:
labels = data[label_column]
else:
labels = values.index
else:
values = data
labels = data.index
color_column = None # ignore color_column for Series
(fig, ax) = _plt(figsize=figsize, pos=pos,
rowspan=rowspan, colspan=colspan)
bars = ax.bar(labels, values)
if color_column:
colors = data[color_column]
if pd_types.is_numeric_dtype(colors.dtype):
color_map = plt_cm.get_cmap(cmap)
norm = plt_colors.Normalize(vmin=colors.min(), vmax=colors.max())
for b, cv in zip(bars, colors):
b.set_color(color_map(norm(cv)))
else:
for b, c in zip(bars, colors):
b.set_color(c)
elif color:
if type(color) is str:
for b in bars:
b.set_color(color)
else:
for b, c in zip(bars, cycle(color)):
b.set_color(c)
ax.set_xlabel(_col_label(xlabel, label_column))
ax.set_ylabel(_col_label(ylabel, value_column))
_finish_figure(
fig=fig, ax=ax, title=title, pad=pad,
file_name=file_name, file_dpi=file_dpi)
[docs]def bar_groups(data: pd.DataFrame,
value_column, key_column, keys=None, label_column=None,
color_column=None, cmap=None, color=None,
stacked=False, relative=False,
xlabel=None, ylabel=None, title=None, legend=True,
figsize=(10, 4), pad=1, pos=(0, 0), rowspan=1, colspan=1,
file_name=None, file_dpi=300):
"""
Display a bar chart with grouped bars from columns in a DataFrame.
:param data: A Pandas DataFrame.
:param value_column: The column with the values for the bars height.
:param key_column: The column with the key to group by.
:param keys: A list with group keys to select. (optional)
By default the group keys are taken from the key
column and sorted alphabetically.
:param label_column: The column with the labels for the bars. (optional)
:param color_column: The column with a numeric value for choosing
a color from a color map or strings
for explicit colors. (optional)
:param cmap: The name of a color map to use with `color_column`.
(optional)
:param color: A list or dict with colors for the groups. (optional)
`color_column` superseeds `color`.
:param stacked: A switch to stack the bars. (optional)
:param relative: A switch to show relative portions with stacked bars.
(optional)
:param legend: A switch to control the visibility of the legend.
(optional)
:param xlabel: The label for the X axis. (optional)
:param ylabel: The label for the Y axis. (optional)
:param title: The title of the plot. (optional)
:param figsize: The figure size in inches. (optional)
:param pad: Padding around the figure. (optional)
:param pos: The position in the grid of a multiplot. (optional)
:param rowspan: The number of rows to span in the grid
of a multiplot. (optional)
:param colspan: The number of columns to span in the grid
of a multiplot. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
all_columns = [value_column, key_column, label_column, color_column]
columns = set(c for c in all_columns if c)
data = data.loc[:, columns].dropna()
if keys is None:
keys = data[key_column].drop_duplicates().sort_values().values
groups = {k: data.loc[data[key_column] == k, :] for k in keys}
first_group = groups[keys[0]]
first_labels = first_group[label_column] if label_column else first_group.index
gs = len(keys)
gd = gs + 0.5
if stacked:
pos = list(np.arange(0, len(first_group)))
if relative:
label_scale = 100.0 / sum(g[value_column].values for g in groups.values())
else:
label_scale = [1.0] * len(first_labels)
else:
pos = {k: list(np.arange(i, i + len(first_group) * gd, gd))
for i, k in enumerate(keys)}
if color_column:
color_values = data[color_column]
if pd_types.is_numeric_dtype(color_values.dtype):
color_map = plt_cm.get_cmap(cmap)
norm = plt_colors.Normalize(vmin=color_values.min(), vmax=color_values.max())
(fig, ax) = _plt(figsize=figsize, pos=pos,
rowspan=rowspan, colspan=colspan)
legend_handles = []
last_key = None
for k, c in zip(keys, _build_key_colors(keys, color)):
g = groups[k]
if stacked:
p = pos
if last_key:
bars = ax.bar(p, g[value_column].values * label_scale, color=c,
bottom=groups[last_key][value_column].values * label_scale)
else:
bars = ax.bar(p, g[value_column].values * label_scale, color=c)
last_key = k
else:
bars = ax.bar(pos[k], g[value_column].values, color=c, width=1)
if color_column:
colors = g[color_column]
if pd_types.is_numeric_dtype(colors.dtype):
for b, cv in zip(bars, colors):
b.set_color(color_map(norm(cv)))
else:
for b, c in zip(bars, colors):
b.set_color(c)
else:
legend_handles.append(mlines.Line2D(
[], [], color=c, linewidth=8, label=k))
def group_labels_unique(gl):
ls = gl[0]
for ls2 in gl[1:]:
if ls != ls2:
return False
return True
if stacked:
ax.set_xticks(pos)
ax.set_xticklabels(first_labels)
else:
if label_column:
group_labels = [tuple(groups[k][label_column]) for k in keys]
if group_labels_unique(group_labels):
pos = list(np.arange((gs - 1) * 0.5, (gs - 1) * 0.5 + gd * len(first_group), gd))
ax.set_xticks(pos)
ax.set_xticklabels(first_labels)
else:
ax.set_xticks(list(chain(*(pos[k] for k in keys))))
ax.set_xticklabels(list(chain(*(groups[k][label_column] for k in keys))))
else:
ax.set_xticks(list(chain(*(pos[k] for k in keys))))
ax.set_xticklabels(list(chain(*(groups[k].index for k in keys))))
ax.set_xlabel(_col_label(xlabel, label_column))
if stacked and relative:
ax.set_ylabel(_col_label(ylabel, value_column) + ' (%)')
else:
ax.set_ylabel(_col_label(ylabel, value_column))
if legend and legend_handles:
ax.legend(handles=legend_handles)
_finish_figure(
fig=fig, ax=ax, title=title, pad=pad,
file_name=file_name, file_dpi=file_dpi)
[docs]def hist(data: Union[pd.DataFrame, pd.Series],
column=None, key_column=None,
bins=35, ticks=None, xmin=None, xmax=None, ylog=False,
color=None, cumulative=False, stacked=False,
xlabel=None, ylabel=None, title=None, legend=True,
figsize=(10, 4), pad=1, pos=(0, 0), rowspan=1, colspan=1,
file_name=None, file_dpi=300):
"""
Display a histogram for the values of one column in a DataFrame
or a Series.
If using a DataFrame, optionally group the values by another key column.
:param data: A Pandas DataFrame or Series.
:param column: The column to build the histogram of.
:param key_column: The column to group the values by. (optional)
:param bins: The bins of the histogram (int or sequence or str).
(optional)
See argument `bins` of `matplotlib.axes.Axes.hist()`
for more details.
:param ticks: A sequence of tick positions on the X axis. (optional)
:param xmin: The lower limit for displayed values (inclusive).
(optional)
:param xmax: The upper limit for displayed values (exclusive).
(optional)
:param ylog: A switch to use a logarithmic scale on the Y axis
(optional)
:param color: A color for all bars, a list with a color per bar
(cycled if too short), or a list with one color
per key if `key_column` is used. (optional)
:param cumulative: A switch to activate cumulative summing. (optional)
:param stacked: A switch to stack bars if `key_column` is used.
(optional)
:param xlabel: The label for the X axis. (optional)
:param ylabel: The label for the Y axis. (optional)
:param title: The title of the plot. (optional)
:param legend: A switch to control the visibility of the legend.
(optional)
:param figsize: The figure size in inches. (optional)
:param pad: Padding around the figure. (optional)
:param pos: The position in the grid of a multiplot. (optional)
:param rowspan: The number of rows to span in the grid
of a multiplot. (optional)
:param colspan: The number of columns to span in the grid
of a multiplot. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
def prep_values(s):
s = s.dropna()
if xmin is not None:
s = s.loc[s >= xmin]
if xmax is not None:
s = s.loc[s <= xmax]
return s.values
if isinstance(data, pd.DataFrame):
# data is a DataFrame
if key_column:
grouped = data.groupby(key_column)
labels = grouped.groups.keys()
x = [prep_values(grouped.get_group(g)[column]) for g in labels]
else:
labels = None
x = prep_values(data[column])
else:
# assume data is a Series
labels = None
x = prep_values(data)
(fig, ax) = _plt(figsize=figsize, pos=pos,
rowspan=rowspan, colspan=colspan)
if labels:
if isinstance(color, str):
color = list(repeat(color, len(labels)))
elif isinstance(color, Mapping):
color = [color.get(l) or next(plt.gca()._get_lines.prop_cycler)['color']
for l in labels]
elif isinstance(color, Iterable):
color = list(islice(cycle(color), len(labels)))
if not labels and not isinstance(color, str) and isinstance(color, Iterable):
colors = color
color = colors[0]
else:
colors = None
N, bins, patches = ax.hist(
x, label=labels, bins=bins, cumulative=cumulative,
stacked=stacked, color=color)
if colors:
colors = list(islice(cycle(colors), len(patches)))
for p, c in zip(patches, colors):
p.set_facecolor(c)
ax.set_xlim(left=xmin, right=xmax)
if ticks is not None:
ax.set_xticks(ticks)
if ylog:
ax.set_yscale('log', nonposy='clip')
ax.set_xlabel(_col_label(xlabel, column))
ax.set_ylabel(_col_label(ylabel, 'count'))
if legend and key_column:
ax.legend()
_finish_figure(
fig=fig, ax=ax, title=title, pad=pad,
file_name=file_name, file_dpi=file_dpi)
[docs]def hist2d(data: pd.DataFrame, xcolumn, ycolumn,
xmin=None, xmax=None, ymin=None, ymax=None,
bins=20, xticks=None, yticks=None,
cmap='Blues', colorbar=True,
xlabel=None, ylabel=None, title=None,
figsize=(7.5, 6), pad=1, pos=(0, 0), rowspan=1, colspan=1,
file_name=None, file_dpi=300):
"""
Displays a 2-dimensional histogram (heatmap).
:param data: A Pandas DataFrame.
:param xcolumn: The column for the horizontal dimension.
:param ycolumn: The column for the vertical dimension.
:param xmin: The lower limit for displayed values
in the horizontal dimension (inclusive). (optional)
:param xmax: The upper limit for displayed values
in the horizontal dimension (exclusive). (optional)
:param ymin: The lower limit for displayed values
in the vertical dimension (inclusive). (optional)
:param ymax: The upper limit for displayed values
in the vertical dimension (exclusive). (optional)
:param bins: None or int or [int, int] or array_like or [array, array].
(optional)
See `matplotlib.pyplot.hist2d()` for more info.
:param xticks: A sequence of tick positions on the X axis. (optional)
:param yticks: A sequence of tick positions on the Y axis. (optional)
:param cmap: A Matplotlib Colormap or the name of a color map.
(optional)
See `matplotlib.pyplot.hist2d()` for more info.
:param colorbar: A switch to control if a colorbar is shown. (optional)
:param xlabel: A label for the X axis. (optional)
:param ylabel: A label for Y axis. (optional)
:param title: A title for the plot. (optional)
:param figsize: The figure size in inches. (optional)
:param pad: Padding around the figure. (optional)
:param pos: The position in the grid of a multiplot. (optional)
:param rowspan: The number of rows to span in the grid
of a multiplot. (optional)
:param colspan: The number of columns to span in the grid
of a multiplot. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
data = data.loc[:, [xcolumn, ycolumn]].dropna()
if xmin is not None:
data = data.loc[data[xcolumn] >= xmin]
if xmax is not None:
data = data.loc[data[xcolumn] < xmax]
if ymin is not None:
data = data.loc[data[ycolumn] >= ymin]
if ymax is not None:
data = data.loc[data[ycolumn] < ymax]
x = data.loc[:, xcolumn]
y = data.loc[:, ycolumn]
if x.empty or y.empty:
return
xmin = xmin if xmin is not None else x.min()
xmax = xmax if xmax is not None else x.max()
ymin = ymin if ymin is not None else y.min()
ymax = ymax if ymax is not None else y.max()
r = [[xmin, xmax], [ymin, ymax]]
(fig, ax) = _plt(figsize=figsize, pos=pos,
rowspan=rowspan, colspan=colspan)
(*_, image) = ax.hist2d(x, y, cmap=cmap, range=r, bins=bins, cmin=1)
if xticks is not None:
ax.set_xticks(xticks)
if yticks is not None:
ax.set_yticks(yticks)
ax.set_xlabel(_col_label(xlabel, xcolumn))
ax.set_ylabel(_col_label(ylabel, ycolumn))
if colorbar:
divider = axg1.make_axes_locatable(ax)
cb_ax = divider.append_axes('right', '5%', pad='5%')
plt.colorbar(image, cax=cb_ax)
_finish_figure(
fig=fig, ax=ax, title=title, pad=pad,
file_name=file_name, file_dpi=file_dpi)
[docs]def scatter(data: pd.DataFrame, xcolumn, ycolumn,
size_column=None, color_column=None,
xmin=None, xmax=None, ymin=None, ymax=None,
xticks=None, yticks=None,
size=1, color=None, cmap='rainbow', colorbar=True,
xlabel=None, ylabel=None, title=None,
figsize=(9.8, 8), pad=1, pos=(0, 0), rowspan=1, colspan=1,
file_name=None, file_dpi=300):
"""
Display a 2-dimensional scatter plot.
:param data: A Pandas DataFrame
:param xcolumn: The column for the horizontal dimension.
:param ycolumn: The column for the vertical dimension.
:param size_column: A column for the marker size. (optional)
:param color_column: A column with values for the marker color. (optional)
:param xmin: The lower limit for displayed values
in the horizontal dimension. (optional)
:param xmax: The upper limit for displayed values
in the horizontal dimension. (optional)
:param ymin: The lower limit for displayed values
in the vertical dimension. (optional)
:param ymax: The upper limit for displayed values
in the vertical dimension. (optional)
:param xticks: A sequence of tick positions on the X axis.
(optional)
:param yticks: A sequence of tick positions on the Y axis.
(optional)
:param size: A factor to the marker size. (optional)
:param color: A color for the markers. (optional)
Gets overridden by `color_column`.
:param cmap: A Matplotlib Colormap or the name of a color map.
Is used in combination with `color_column`. (optional)
See `matplotlib.pyplot.scatter()` for more info.
:param colorbar: A switch to control if a colorbar is shown. (optional)
:param xlabel: A label for the X axis. (optional)
:param ylabel: A label for Y axis. (optional)
:param title: A title for the plot. (optional)
:param figsize: The figure size in inches. (optional)
:param pad: Padding around the figure. (optional)
:param pos: The position in the grid of a multiplot. (optional)
:param rowspan: The number of rows to span in the grid
of a multiplot. (optional)
:param colspan: The number of columns to span in the grid
of a multiplot. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
columns = list(set(c for c in [xcolumn, ycolumn, size_column, color_column]
if c and c in data.columns))
data = data.loc[:, columns].dropna()
x = data[xcolumn]
y = data[ycolumn]
s = (data[size_column] if size_column else 20) * size
c = color
if color_column:
c = data[color_column]
if not pd_types.is_numeric_dtype(c.dtype):
cmap = None
colorbar = False
(fig, ax) = _plt(figsize=figsize, pos=pos,
rowspan=rowspan, colspan=colspan)
marker = ax.scatter(x, y, s=s, c=c, marker='o', cmap=cmap)
ax.set_xlim(left=xmin, right=xmax)
ax.set_ylim(bottom=ymin, top=ymax)
if xticks is not None:
ax.set_xticks(xticks)
if yticks is not None:
ax.set_yticks(yticks)
ax.set_xlabel(_col_label(xlabel, xcolumn))
ax.set_ylabel(_col_label(ylabel, ycolumn))
if color_column and colorbar:
divider = axg1.make_axes_locatable(ax)
cb_ax = divider.append_axes('right', '5%', pad='5%')
plt.colorbar(marker, cax=cb_ax)
_finish_figure(
fig=fig, ax=ax, title=title, pad=pad,
file_name=file_name, file_dpi=file_dpi)
[docs]def scatter_map(data: pd.DataFrame,
longitude_column='longitude', latitude_column='latitude',
region=None, autofit=False,
projection='merc',
map_resolution='i', grid=(1, 2),
map_style=None, map_style_attributes=None,
size_column=None, size=1, size_mode=None,
color_column=None, color='blue', cmap='YlGnBu', colorbar=True,
title=None,
figsize=(10, 10), pad=1, pos=(0, 0), rowspan=1, colspan=1,
file_name=None, file_dpi=300):
"""
Displays a scatter plot on a geographical map.
:param data: A Pandas DataFrame.
:param longitude_column:
The column with the longitudes. (optional)
:param latitude_column:
The column with the latitudes. (optional)
:param region: The geographic region to plot. (optional)
A iterable with four elements:
lower left corner latitude,
lower left corner longitude,
upper right corner latitude,
and upper right corner longitude.
:param autofit: A switch to automatically zoom to a region,
showing all markers. (optional)
:param grid: A pair of distances for grid lines (lat, lon).
(optional)
:param projection: The named projection of the map.
See https://matplotlib.org/basemap/users/mapsetup.html
:param map_style: The name of a style. (optional)
:param map_style_attributes:
A dict with style attributes. (optional)
:param map_resolution:
The resolution of geographical and political features
on the map: crude `c`, low `l`, intermediate `i`,
high `h`, or full `f`. (optional)
:param size_column: A column with marker sizes. (optional)
:param size: A factor to the marker size. (optional)
:param size_mode: The mode for applying the size: `area` or `radius`.
(optional)
:param color_column: A column with values for the marker color. (optional)
:param color: A color for the markers. (optional)
Gets overridden by `color_column`.
:param cmap: A Matplotlib Colormap or the name of a color map.
Is used in combination with `color_column`. (optional)
See `matplotlib.pyplot.scatter()` for more info.
:param colorbar: A switch to control if a colorbar is shown. (optional)
:param title: A title for the plot. (optional)
:param figsize: The figure size in inches. (optional)
:param pad: Padding around the figure. (optional)
:param pos: The position in the grid of a multiplot. (optional)
:param rowspan: The number of rows to span in the grid
of a multiplot. (optional)
:param colspan: The number of columns to span in the grid
of a multiplot. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
from .basemap import base_map, lat_lon_region
columns = list(set(c for c in [longitude_column, latitude_column,
size_column, color_column]
if c and c in data.columns))
data = data.loc[:, columns].dropna()
lon = data.loc[:, longitude_column]
lat = data.loc[:, latitude_column]
s = (data.loc[:, size_column].values if size_column else 1) * size
if size_mode == 'radius':
s = np.power(s, 2.0) * pi
if size_mode == 'area':
pass
c = color
if color_column:
c = data[color_column]
if not pd_types.is_numeric_dtype(c.dtype):
cmap = None
colorbar = False
if autofit or region is None:
region = [lat.min(), lon.min(), lat.max(), lon.max()]
lat_margin = abs(region[2] - region[0]) * 0.15
lon_margin = abs(region[3] - region[1]) * 0.15
region[0] -= lat_margin
region[1] -= lon_margin
region[2] += lat_margin
region[3] += lon_margin
if region[2] - region[0] > 180:
region[0], region[2] = region[2], region[0]
(fig, ax) = _plt(figsize=figsize, pos=pos,
rowspan=rowspan, colspan=colspan)
m = base_map(lat_lon_region(*region), projection=projection,
resolution=map_resolution, grid=grid,
style_name=map_style, style_attributes=map_style_attributes,
ax=ax)
marker = m.scatter(list(lon.values), list(lat.values), latlon=True,
s=s, c=c, marker='o', cmap=cmap, zorder=10)
if color_column and colorbar:
divider = axg1.make_axes_locatable(ax)
cb_ax = divider.append_axes('right', '5%', pad='5%')
plt.colorbar(marker, cax=cb_ax)
_finish_figure(
fig=fig, ax=ax, title=title, pad=pad,
file_name=file_name, file_dpi=file_dpi)
def _moving_average(indices: np.ndarray, values: np.ndarray, window):
if len(indices) != len(values):
raise Exception('indices and values do not have the same size')
weights = np.repeat(1.0, window) / window # kernel
means = np.convolve(values, weights, 'valid')
start = floor(window / 2)
end = len(indices) - ceil(window / 2) + 1
sub_indices = indices[start:end]
return sub_indices, means
def _interpolate(indices: np.ndarray, values: np.ndarray, step, kind):
f = interpolate.interp1d(indices, values, kind=kind)
x = np.arange(indices[0], indices[-1], step)
return x, f(x)
[docs]def line(data: Union[pd.DataFrame, pd.Series],
column=None, xcolumn=None,
color=None, linewidth=2,
avg_window=None, interpolation_step=None, interpolation_kind='quadratic',
xmin=None, xmax=None, ymin=None, ymax=None,
xticks=None, yticks=None,
xlabel=None, ylabel=None, title=None,
figsize=(10, 5), pad=1, pos=(0, 0), rowspan=1, colspan=1,
file_name=None, file_dpi=300):
"""
Display a line from values in one column of a DataFrame or a Series.
If `data` is a Series, the index will be used for the horizontal dimension.
:param data: A Pandas DataFrame or a Series.
:param column: The column with the values to display as a line.
The values are used as vertical dimension.
:param xcolumn: A column with values for the horizontal dimension.
(optional)
:param color: A color for the line. (optional)
:param linewidth: The width of the line.
:param avg_window: The size of a window for smoothing the values
with a sliding average. (optional)
:param interpolate_step:
A step size in the horizontal dimension,
for smoothing the line with interpolation.
:param interpolate_kind:
The kind of interpolation to use:
`quadratic` or `cubic`. (optional)
Has an effect only if `interpolation_step` is used.
:param xmin: The lower limit for displayed values
in the horizontal dimension. (optional)
:param xmax: The upper limit for displayed values
in the horizontal dimension. (optional)
:param ymin: The lower limit for displayed values
in the vertical dimension. (optional)
:param ymax: The upper limit for displayed values
in the vertical dimension. (optional)
:param xticks: A sequence of tick positions on the X axis. (optional)
:param yticks: A sequence of tick positions on the Y axis. (optional)
:param xlabel: A label for the X axis. (optional)
:param ylabel: A label for Y axis. (optional)
:param title: A title for the plot. (optional)
:param figsize: The figure size in inches. (optional)
:param pad: Padding around the figure. (optional)
:param pos: The position in the grid of a multiplot. (optional)
:param rowspan: The number of rows to span in the grid
of a multiplot. (optional)
:param colspan: The number of columns to span in the grid
of a multiplot. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
(fig, ax) = _plt(figsize=figsize, pos=pos,
rowspan=rowspan, colspan=colspan)
def plot_line(d, c=None):
if isinstance(d, pd.DataFrame):
x = d[xcolumn].values if xcolumn else d.index.values
y = d[column].values
else:
x = d.index.values
y = d.values
if avg_window:
x, y = _moving_average(x, y, avg_window)
if interpolation_step:
x, y = _interpolate(x, y, interpolation_step, interpolation_kind)
ax.plot(x, y, color=c, linewidth=linewidth)
if isinstance(data, pd.DataFrame):
# data is DataFrame
columns = set()
columns.add(column)
if xcolumn:
columns.add(xcolumn)
data = data.loc[:, columns].dropna()
else:
# assume data is Series
pass
plot_line(data, c=color)
ax.set_xlim(left=xmin, right=xmax)
ax.set_ylim(bottom=ymin, top=ymax)
if xticks is not None:
ax.set_xticks(xticks)
if yticks is not None:
ax.set_yticks(yticks)
ax.set_xlabel(_col_label(xlabel, xcolumn))
ax.set_ylabel(_col_label(ylabel, column))
_finish_figure(
fig=fig, ax=ax, title=title, pad=pad,
file_name=file_name, file_dpi=file_dpi)
[docs]def lines(data: pd.DataFrame, column, xcolumn=None,
key_column=None, min_n=None, label_column=None,
color=None, linewidth=2,
avg_window=None, interpolation_step=None, interpolation_kind='quadratic',
xmin=None, xmax=None, ymin=None, ymax=None,
xticks=None, yticks=None,
xlabel=None, ylabel=None, title=None, legend=True,
figsize=(10, 5), pad=1, pos=(0, 0), rowspan=1, colspan=1,
file_name=None, file_dpi=300):
"""
Display line(s) from values in one column of a DataFrame.
:param data: A Pandas DataFrame.
:param column: The column with the values to display as a line.
The values are used as vertical dimension.
:param xcolumn: A column with values for the horizontal dimension.
(optional)
:param key_column: A column for grouping without labels.
:param label_column: A column for grouping with labels.
:param min_n: The minimum number of values, required in a group
for it to get drawn by a line. (optional)
:param color: A color for the line(s). (optional)
:param linewidth: The width of the line(s).
:param avg_window: The size of a window for smoothing the values
with a sliding average. (optional)
:param interpolate_step:
A step size in the horizontal dimension,
for smoothing the line with interpolation.
:param interpolate_kind:
The kind of interpolation to use:
`quadratic` or `cubic`. (optional)
Has an effect only if `interpolation_step` is used.
:param xmin: The lower limit for displayed values
in the horizontal dimension. (optional)
:param xmax: The upper limit for displayed values
in the horizontal dimension. (optional)
:param ymin: The lower limit for displayed values
in the vertical dimension. (optional)
:param ymax: The upper limit for displayed values
in the vertical dimension. (optional)
:param xticks: A sequence of tick positions on the X axis. (optional)
:param yticks: A sequence of tick positions on the Y axis. (optional)
:param xlabel: A label for the X axis. (optional)
:param ylabel: A label for Y axis. (optional)
:param title: A title for the plot. (optional)
:param legend: A switch to control the appearance of a legend.
(optional)
:param figsize: The figure size in inches. (optional)
:param pad: Padding around the figure. (optional)
:param pos: The position in the grid of a multiplot. (optional)
:param rowspan: The number of rows to span in the grid
of a multiplot. (optional)
:param colspan: The number of columns to span in the grid
of a multiplot. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
(fig, ax) = _plt(figsize=figsize, pos=pos,
rowspan=rowspan, colspan=colspan)
legend_handles = []
columns = set()
columns.add(column)
if xcolumn:
columns.add(xcolumn)
if label_column and not key_column:
key_column = label_column
def plot_line(d, c=None, l=None):
if min_n and len(d) < min_n:
return
x = d.loc[:, xcolumn].values if xcolumn else d.index.values
y = d.loc[:, column].values
if avg_window:
x, y = _moving_average(x, y, avg_window)
if interpolation_step:
x, y = _interpolate(x, y, interpolation_step, interpolation_kind)
ax.plot(x, y, label=l, color=c, linewidth=linewidth)
if key_column:
columns.add(key_column)
if label_column:
columns.add(label_column)
data = data.loc[:, columns].dropna()
lgrouped = data.groupby(label_column)
keys = sorted(lgrouped.groups.keys())
for label, c in zip(keys, _build_key_colors(keys, color)):
ldata = lgrouped.get_group(label)
legend_handles.append(mlines.Line2D(
[], [], color=c, linewidth=linewidth, label=label))
grouped = ldata.groupby(key_column)
for k in grouped.groups.keys():
plot_line(grouped.get_group(k), c=c, l=label)
else:
data = data.loc[:, columns].dropna()
grouped = data.groupby(key_column)
keys = grouped.groups.keys()
for k, c in zip(keys, _build_key_colors(keys, color)):
plot_line(grouped.get_group(k), c=c)
else:
data = data.loc[:, columns].dropna()
plot_line(data, c=color)
ax.set_xlim(left=xmin, right=xmax)
ax.set_ylim(bottom=ymin, top=ymax)
if xticks is not None:
ax.set_xticks(xticks)
if yticks is not None:
ax.set_yticks(yticks)
ax.set_xlabel(_col_label(xlabel, xcolumn))
ax.set_ylabel(_col_label(ylabel, column))
if legend and legend_handles:
ax.legend(handles=legend_handles)
_finish_figure(
fig=fig, ax=ax, title=title, pad=pad,
file_name=file_name, file_dpi=file_dpi)
[docs]def scatter_matrix(data: pd.DataFrame, columns=None,
mins=None, maxs=None, bins=None, ticks=None,
sample=None, random_state=None,
key_column=None, color=None,
subplot_size=2, pad=1, w_pad=1.0, h_pad=1.75,
file_name=None, file_dpi=300):
"""
Plots a matrix of scatter plots and histograms for a number of columns
from a Pandas DataFrame.
Warning: This function cannot be used between `begin()` and `end()` as part
of another multiplot.
:param data: A Pandas DataFrame.
:param columns: The columns to include into the matrix. (optional)
:param key_column: A column used to build groups. (optional)
:param color: A list or dict with colors for the groups. (optional)
:param mins: A dict, mapping column names to minimal values.
(optional)
:param maxs: A dict, mapping column names to maximal values.
(optional)
:param sample: A ratio between 0 and 1 to show a random subset
in the scatter plots. (optional)
:param random_state: The initial random state for selecting a subset.
(optional)
:param bins: A dict, mapping column names to bins. (optional)
:param ticks: A dict, mapping column names to ticks. (optional)
:param subplot_size: The edge length for the subplots. (optional)
:param pad: Padding around the figure. (optional)
:param w_pad: Horizontal space between subplots. (optional)
:param h_pad: Vertical space between subplots. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
if _in_multiplot():
raise Exception("There is already an open figure. "
"You must use this function outside of a begin()-end()-block?")
if columns is None:
columns = data.columns.values
cn = len(columns)
if key_column:
grouped = data.groupby(key_column)
labels = grouped.groups.keys()
if isinstance(color, Mapping):
color = [color.get(l) or next(plt.gca()._get_lines.prop_cycler)['color']
for l in labels]
elif isinstance(color, Iterable):
color = list(islice(cycle(color), len(labels)))
else:
color = [next(plt.gca()._get_lines.prop_cycler)['color']
for l in labels]
_ = plt.close()
label_colors = dict(zip(labels, color))
data_color = data[key_column].map(label_colors)
data = data.assign(scatter_matrix_color=data_color)
else:
label_colors = color
if sample is not None and sample != 1.0:
subset = data.sample(frac=min(1.0, max(0.0, sample)), random_state=random_state)
else:
subset = data
begin(grid=(cn, cn), figsize=(cn * subplot_size, cn * subplot_size))
try:
for iy, cy in enumerate(columns):
ymin = mins.get(cy) if mins is not None else None
ymax = maxs.get(cy) if maxs is not None else None
ybins = bins.get(cy) if bins is not None else None
yticks = ticks.get(cy) if ticks is not None else None
for ix, cx in enumerate(columns):
xmin = mins.get(cx) if mins is not None else None
xmax = maxs.get(cx) if maxs is not None else None
xticks = ticks.get(cx) if ticks is not None else None
ylabel = cy if ix == 0 else ""
xlabel = cx if iy == cn - 1 else ""
if cy != cx:
scatter(subset, xcolumn=cx, ycolumn=cy,
color_column=('scatter_matrix_color' if key_column else None),
color=(None if key_column else color),
xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax,
xticks=xticks, yticks=yticks,
xlabel=xlabel, ylabel=ylabel,
pos=(iy, ix))
else:
hist(data, cx, key_column=key_column, color=label_colors,
stacked=True, legend=False,
xmin=xmin, xmax=xmax, bins=(ybins or 35), ticks=xticks,
xlabel=xlabel, ylabel=ylabel,
pos=(iy, ix))
finally:
end(pad=pad, h_pad=h_pad, w_pad=w_pad,
file_name=file_name, file_dpi=file_dpi)
[docs]def hist2d_matrix(data: pd.DataFrame, columns=None,
mins=None, maxs=None, bins=None, ticks=None,
subplot_size=2, pad=1, w_pad=1.0, h_pad=1.75, cmap='Blues',
file_name=None, file_dpi=300):
"""
Plots a matrix of 2D histogram plots and histograms for a number of columns
from a Pandas DataFrame.
Warning: This function cannot be used between `begin()` and `end()` as part
of another multiplot.
:param data: A Pandas DataFrame.
:param columns: The columns to include into the matrix. (optional)
:param mins: A dict, mapping column names to minimal values.
(optional)
:param maxs: A dict, mapping column names to maximal values.
(optional)
:param bins: A dict, mapping column names to bins. (optional)
:param ticks: A dict, mapping column names to ticks. (optional)
:param subplot_size: The edge length for the subplots. (optional)
:param pad: Padding around the figure. (optional)
:param w_pad: Horizontal space between subplots. (optional)
:param h_pad: Vertical space between subplots. (optional)
:param cmap: The color map to use. (optional)
:param file_name: A path to a file to save the plot in. (optional)
:param file_dpi: A resolution to render the saved plot. (optional)
"""
if _in_multiplot():
raise Exception("There is already an open figure. "
"You must use this function outside of a begin()-end()-block?")
if columns is None:
columns = data.columns.values
cn = len(columns)
begin(grid=(cn, cn), figsize=(cn * subplot_size, cn * subplot_size))
try:
for iy, cy in enumerate(columns):
ymin = mins.get(cy) if mins is not None else None
ymax = maxs.get(cy) if maxs is not None else None
ybins = bins.get(cy) if bins is not None else None
yticks = ticks.get(cy) if ticks is not None else None
for ix, cx in enumerate(columns):
xmin = mins.get(cx) if mins is not None else None
xmax = maxs.get(cx) if maxs is not None else None
xbins = bins.get(cx) if bins is not None else None
xticks = ticks.get(cx) if ticks is not None else None
ylabel = cy if ix == 0 else ""
xlabel = cx if iy == cn - 1 else ""
if cy != cx:
hist2d(data, xcolumn=cx, ycolumn=cy, cmap=cmap,
bins=(xbins or 20, ybins or 20),
xticks=xticks, yticks=yticks,
xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax,
xlabel=xlabel, ylabel=ylabel, colorbar=False,
pos=(iy, ix))
else:
hist(data, cx,
xmin=xmin, xmax=xmax,
bins=(xbins or 35), ticks=xticks,
xlabel=xlabel, ylabel=ylabel,
pos=(iy, ix))
finally:
end(pad=pad, h_pad=h_pad, w_pad=w_pad,
file_name=file_name, file_dpi=file_dpi)