topostats.plotting

Plotting and summary of TopoStats output statistics.

Attributes

LOGGER

Classes

TopoSum

Class for summarising grain statistics in plots.

Functions

toposum(→ Dict)	Process plotting and summarisation of data.
run_toposum([args])	Run Plotting

Module Contents

topostats.plotting.LOGGER

class topostats.plotting.TopoSum(df: pandas.DataFrame = None, base_dir: str | pathlib.Path = None, csv_file: str | pathlib.Path = None, stat_to_sum: str = None, molecule_id: str = 'molecule_number', image_id: str = 'image', hist: bool = True, stat: str = 'count', bins: int = 12, kde: bool = True, cut: float = 20, figsize: tuple = (16, 9), alpha: float = 0.5, palette: str = 'deep', file_ext: str = 'png', output_dir: str | pathlib.Path = '.', var_to_label: dict = None, hue: str = 'basename')

Class for summarising grain statistics in plots.

df

base_dir

stat_to_sum

molecule_id

image_id

hist

bins

stat

kde

cut

figsize

alpha

palette

file_ext

output_dir

var_to_label

hue

melted_data = None

summary_data = None

label = None

_setup_figure()

Setup Matplotlib figure and axes.

_outfile(plot_suffix: str) → str

Generate the output file name with the appropriate suffix.

Parameters:

plot_suffix (str) – The suffix to append to the output file.

Returns:

Concanenated string of the outfile and plot_suffix.

Return type:

str

sns_plot() → Tuple[matplotlib.pyplot.Figure, matplotlib.pyplot.Axes] | None

Plot the distribution of one or more statistics as either histogram, kernel density estimates or both. Uses base Seaborn.

Returns:

Tuple of Matplotlib figure and axes if plotting is successful, None otherwise.

Return type:

Optional[Union[Tuple[plt.Figure, plt.Axes], None]]

sns_violinplot() → None

Violin plot of data.

static melt_data(df: pandas.DataFrame, stat_to_summarize: str, var_to_label: dict) → pandas.DataFrame

Melt a dataframe into long format for plotting with Seaborn.

set_xlim(percent: float = 0.1) → None

Set the range of the x-axis.

Parameters:

• percent (float) – Percentage of the observed range by which to extend the x-axis. Only used if supplied range is outside the

• values. (observed)

set_palette()

Set the color palette.

save_plot(outfile: pathlib.Path) → None

Save the plot to the output_dir

Parameters:

outfile (str) – Output file name to save figure to.

_set_label(var: str)

Get the label based on the column name(s).

Parameters:

var (str) – The variable for which a label is required.

topostats.plotting.toposum(config: dict) → Dict

Process plotting and summarisation of data.

Parameters:

config (dict) – Dictionary of summarisation options.

Returns:

Dictionary of nested dictionaries. Each variable has its own dictionary with keys ‘dist’ and ‘violin’ which

contain distribution like plots and violin plots respectively (if the later are required). Each ‘dist’ and

’violin’ is itself a dictionary with two elements ‘figures’ and ‘axes’ which correspond to MatplotLib ‘fig’ and ‘ax’ for that plot.

Return type:

Dict

topostats.plotting.run_toposum(args=None)

Run Plotting