Python - pyDicePlot

The pyDicePlot package allows you to create visualizations (DicePlots) for datasets with more than two categorical variables and additional continuous variables. This tool is particularly useful for exploring complex categorical data and their relationships with continuous variables.

Requirements and installation

Using Conda

To set up the environment and install dependencies:

conda create --name pyDicePlot python=3
conda activate pyDicePlot
pip install -r requirements.txt

Installation via pip

To install the package via pip, run:

from the base directory.

Sample Output

alt:

Sample Dice with 3 categories Plot

Figure: A sample DicePlot generated using the pyDicePlot package.

DicePlot

Here is a simple example of how to use the pydiceplot package using dummy data. The example shows a dummy dataframe containing three hypothetical categorical variables: CellType, Pathway, and PathologyVariable. The Group variable is used to assign different colors to the pathways.

from pydiceplot import dice_plot
from pydiceplot.plots.backends._dice_utils import (get_diceplot_example_data,
                                                   get_example_group_colors,
                                                   get_example_cat_c_colors)
import pydiceplot

#Set the backend for pydiceplot
pydiceplot.set_backend("matplotlib")
pydiceplot.set_backend("plotly")

if __name__ == "__main__":
    plot_path = "./plots"

    # define colors for the example plot


    # Generate and save dice plots for different numbers of pathology variables
    for n in [2,3, 4, 5, 6]:
        # Get the data using the utility function
        # load example data
        data_expanded = get_diceplot_example_data(n)
        group_colors = get_example_group_colors()
        cat_c_colors = get_example_cat_c_colors()
        # Define pathology variables and their colors
        # extract pathology variables and select proper color scale
        pathology_vars = data_expanded["PathologyVariable"].unique()
        current_cat_c_colors = {var: cat_c_colors[var] for var in pathology_vars}

        # Create the dice plot
        title = f"Dice Plot with {n} Pathology Variables"
        fig = dice_plot(
            data=data_expanded,
            cat_a="CellType",
            cat_b="Pathway",
            cat_c="PathologyVariable",
            group="Group", # default is set to None, it will color the boxes plain white
            switch_axis=False,
            title=title,
            cat_c_colors=current_cat_c_colors,
            group_colors=group_colors,  # Include group colors
            max_dice_sides=6  # Adjust if needed
        )

        # Display and save the figure
        fig.show()

Example Usage

Note

Todo

DominoPlot

Note

Todo

Example Usage

Note

Todo