covsirphy.visualization package

Submodules

covsirphy.visualization.bar_plot module

class BarPlot(filename=None, bbox_inches='tight', **kwargs)

Bases: VisualizeBase

Create a bar plot.

Parameters:

• filename (str or None) – filename to save the figure or None (display)

• bbox_inches (str) – bounding box in inches when creating the figure

• kwargs – the other arguments of matplotlib.pyplot.savefig()

line(v=None, h=None, color='black', linestyle=':')

Show vertical/horizontal lines.

Parameters:

• v (list[int/float] or None) – list of x values of vertical lines or None

• h (list[int/float] or None) – list of y values of horizontal lines or None

• color (str) – color of the line

• linestyle (str) – linestyle

plot(data, vertical=True, colormap=None, color_dict=None, **kwargs)

Create bar plot.

Parameters:

• data (pandas.DataFrame or pandas.Series) –

  data to show Index

  labels of the bars

  Columns

  variables to show

• vertical (bool) – whether vertical bar plot (True) or horizontal bar plot (False)

• colormap (str, matplotlib colormap object or None) – colormap, please refer to https://matplotlib.org/examples/color/colormaps_reference.html

• color_dict (dict[str, str] or None) – dictionary of column names (keys) and colors (values)

• kwargs – keyword arguments of pandas.DataFrame.plot()

x_axis(xlabel=None)

Set x axis.

Parameters:

xlabel (str or None) – x-label

y_axis(ylabel='Cases', y_logscale=False, ylim=(0, None), math_scale=True, y_integer=False)

Set x axis.

Parameters:

• ylabel (str or None) – y-label

• y_logscale (bool) – whether use log-scale in y-axis or not

• ylim (tuple(int or float, int or float)) – limit of y domain

• math_scale (bool) – whether use LaTEX or not in y-label

• y_integer (bool) – whether force to show the values as integer or not

Note

If None is included in ylim, the values will be automatically determined by Matplotlib

bar_plot(df, title=None, filename=None, show_legend=True, **kwargs)

Wrapper function: show chronological change of the data.

Parameters:

• data (pandas.DataFrame or pandas.Series) –

  data to show Index

  Date (pandas.Timestamp)

  Columns

  variables to show

• title (str) – title of the figure

• filename (str or None) – filename to save the figure or None (display)

• show_legend (bool) – whether show legend or not

• kwargs – keyword arguments of the following classes and methods. - covsirphy.BarPlot() and its methods, - matplotlib.pyplot.savefig(), matplotlib.pyplot.legend(), - pandas.DataFrame.plot()

covsirphy.visualization.compare_plot module

class ComparePlot(filename=None, bbox_inches='tight', **kwargs)

Bases: VisualizeBase

Compare two groups with specified variables.

Parameters:

• filename (str or None) – filename to save the figure or None (display)

• bbox_inches (str) – bounding box in inches when creating the figure

• kwargs – the other arguments of matplotlib.pyplot.savefig()

plot(data, variables, groups)

Compare two groups with specified variables.

Parameters:

• data (pandas.DataFrame) –

  data to show Index

  x values

  Columns

  y variables to show, “{variable}_{group}” for all combinations of variables and groups

• variables (list[str]) – variables to compare

• groups (list[str]) – the first group name and the second group name

compare_plot(df, variables, groups, filename=None, **kwargs)

Wrapper function: show chronological change of the data.

Parameters:

• df (pandas.DataFrame) –

  data to show Index

  x values

  Columns

  y variables to show, “{variable}_{group}” for all combinations of variables and groups

• variables (list[str]) – variables to compare

• groups (list[str]) – the first group name and the second group name

• filename (str or None) – filename to save the figure or None (display)

• kwargs – keyword arguments of the following classes and methods. - matplotlib.pyplot.savefig() - matplotlib.pyplot.legend()

covsirphy.visualization.line_plot module

class LinePlot(filename=None, bbox_inches='tight', **kwargs)

Bases: VisualizeBase

Create a line plot.

Parameters:

• filename (str or None) – filename to save the figure or None (display)

• bbox_inches (str) – bounding box in inches when creating the figure

• kwargs – the other arguments of matplotlib.pyplot.savefig()

line(v=None, h=None, color='black', linestyle=':')

Show vertical/horizontal lines.

Parameters:

• v (list/tuple[int/float] or None) – list of x values of vertical lines or None

• h (list/tuple[int/float] or None) – list of y values of horizontal lines or None

• color (str) – color of the line

• linestyle (str) – linestyle

plot(data, colormap=None, color_dict=None, **kwargs)

Plot chronological change of the data.

Parameters:

• data (pandas.DataFrame or pandas.Series) –

  data to show Index

  x values

  Columns

  y variables to show

• colormap (str, matplotlib colormap object or None) – colormap, please refer to https://matplotlib.org/examples/color/colormaps_reference.html

• color_dict (dict[str, str] or None) – dictionary of column names (keys) and colors (values)

• kwargs – keyword arguments of pandas.DataFrame.plot()

x_axis(xlabel=None, x_logscale=False, xlim=(None, None))

Set x axis.

Parameters:

• xlabel (str or None) – x-label

• x_logscale (bool) – whether use log-scale in x-axis or not

• xlim (tuple(int or float, int or float)) – limit of x domain

Note

If None is included in xlim, the values will be automatically determined by Matplotlib

y_axis(ylabel='Cases', y_logscale=False, ylim=(0, None), math_scale=True, y_integer=False)

Set x axis.

Parameters:

• ylabel (str or None) – y-label

• y_logscale (bool) – whether use log-scale in y-axis or not

• ylim (tuple(int or float, int or float)) – limit of y domain

• math_scale (bool) – whether use LaTEX or not in y-label

• y_integer (bool) – whether force to show the values as integer or not

Note

If None is included in ylim, the values will be automatically determined by Matplotlib

line_plot(df, title=None, filename=None, show_legend=True, **kwargs)

Wrapper function: show chronological change of the data.

Parameters:

• data (pandas.DataFrame or pandas.Series) –

  data to show Index

  Date (pandas.Timestamp)

  Columns

  variables to show

• title (str) – title of the figure

• filename (str or None) – filename to save the figure or None (display)

• show_legend (bool) – whether show legend or not

• kwargs – keyword arguments of the following classes and methods. - covsirphy.LinePlot() and its methods, - matplotlib.pyplot.savefig(), matplotlib.pyplot.legend(), - pandas.DataFrame.plot()

covsirphy.visualization.scatter_plot module

class ScatterPlot(filename=None, bbox_inches='tight', **kwargs)

Bases: LinePlot

Create a scatter plot.

Parameters:

• filename (str or None) – filename to save the figure or None (display)

• bbox_inches (str) – bounding box in inches when creating the figure

• kwargs – the other arguments of matplotlib.pyplot.savefig()

legend(**kwargs)

ScatterPlot.legend() is not implemented.

legend_hide()

ScatterPlot.legend_hide() is not implemented.

line_straight(p1=None, p2=None, color='black', linestyle=':')

Connect the points with a straight line.

Parameters:

• p1 (tuple(int or float, int or float) or None) – (x, y) of the first point or None (min values)

• p2 (tuple(int or float, int or float) or None) – (x, y) of the second point or None (max values)

• color (str) – color of the line

• linestyle (str) – linestyle

Note

The same line will be show when p1 and p2 is reordered.

plot(data, colormap=None, color_dict=None, **kwargs)

Plot chronological change of the data.

Parameters:

• data (pandas.DataFrame) –

  data to show Index

  reset index

  Columns

  x (int or float): x values y (int or float): y values

• colormap (str, matplotlib colormap object or None) – colormap, please refer to https://matplotlib.org/examples/color/colormaps_reference.html

• color_dict (dict[str, str] or None) – dictionary of column names (keys) and colors (values)

• kwargs – keyword arguments of pandas.DataFrame.plot()

scatter_plot(df, title=None, filename=None, **kwargs)

Wrapper function: show chronological change of the data.

Parameters:

• data (pandas.DataFrame) –

  data to show Index

  reset index

  Columns

  x (int or float): x values y (int or float): y values

• title (str) – title of the figure

• filename (str or None) – filename to save the figure or None (display)

• kwargs – keyword arguments of the following classes and methods. - covsirphy.ScatterPlot() and its methods, - matplotlib.pyplot.savefig(), matplotlib.pyplot.legend(), - pandas.DataFrame.plot()

covsirphy.visualization.vbase module

class VisualizeBase(filename=None, bbox_inches='tight', **kwargs)

Bases: Term

Base class for visualization.

Parameters:

• filename (str or None) – filename to save the figure or None (display)

• bbox_inches (str) – bounding box in inches when creating the figure

• kwargs – the other arguments of matplotlib.pyplot.savefig

property ax

axis

Type:

matplotlib.axis

legend(bbox_to_anchor=(0.5, -0.2), bbox_loc='lower center', ncol=None, **kwargs)

Set legend.

Parameters:

• bbox_to_anchor (tuple(int or float, int or float)) – distance of legend and plot

• bbox_loc (str) – location of legend

• ncol (int or None) – the number of columns that the legend has

• kwargs – keyword arguments of matplotlib.pyplot.legend()

legend_hide()

Hide legend.

plot()

Method for plotting. This will be defined in child classes.

Raises:

NotImplementedError – not implemented

tick_params(**kwargs)

Directly calling matplotlib.pyplot.tick_params, change the appearance of ticks, tick labels and grid lines.

Parameters:

kwargs – arguments of matplotlib.pyplot.tick_params

property title

title of the figure

Type:

str

find_args(func_list, **kwargs)

Find values of enabled arguments of the function from the keyword arguments.

Parameters:

• func_list (list[function] or function) – target function

• kwargs – keyword arguments

Returns:

dict – dictionary of enabled arguments