Source code for moonstone.plot.metadata

import pandas as pd
import plotly.graph_objects as go
from typing import Optional

from moonstone.plot.graphs.bargraph import BarGraph
from moonstone.plot.graphs.histogram import Histogram
from moonstone.utils.plot import (
    add_x_to_plotting_options,
    add_default_titles_to_plotting_options,
)


class PlotMetadataStats:
    """
    Several plots available to visualize metadata.
    """

    def __init__(self, metadata_dataframe: pd.DataFrame):
        self.metadata_df = metadata_dataframe

    def plot_age(
        self,
        bins_size=None,
        plotting_options: dict = None,
        show: Optional[bool] = True,
        output_file: Optional[str] = False,
    ) -> go.Figure:
        """
        method to visualize the age distribution of patients (whose the samples are originated from)

        :param bins_size: size of the bins of the Histogram
        :param show: set to False if you don't want to show the plot
        :param output_file: name of the output file
        :param plotting_options: options of plotting that will override the default setup \n
                                 [!] Make sure the value given to an argument is of the right type \n
                                 options allowed : 'log': `bool` ; 'colorbar': `[str, List[str]]` ;
                                 'tickangle': `[int, float]`
        """
        if plotting_options is None:
            plotting_options = {
                "layout": {
                    "title_text": "Age distribution in the samples",
                    "title_x": 0.5,
                },
                "xaxes": {"title_text": "age"},
                "yaxes": {"title_text": "number of samples"},
            }
        else:
            plotting_options = add_default_titles_to_plotting_options(
                plotting_options,
                "Age distribution in the samples",
                "age",
                "number of samples",
            )

        graph = Histogram(self.metadata_df["age"])

        if bins_size is None:
            bins_size = 1

        fig = graph.plot_one_graph(
            bins_size,
            plotting_options=plotting_options,
            show=show,
            output_file=output_file,
        )

        return fig

    def plot_sex(
        self,
        sex_col: str = "sex",
        plotting_options: dict = None,
        show: Optional[bool] = True,
        output_file: Optional[str] = False,
    ):
        """
        method to visualize the sex distribution of patients (whose the samples are originated from)

        :param show: set to False if you don't want to show the plot
        :param output_file: name of the output file
        :param plotting_options: options of plotting that will override the default setup \n
                                 [!] Make sure the value given to an argument is of the right type \n
                                 options allowed : 'log': `bool` ; 'colorbar': `[str, List[str]]` ;
                                 'tickangle': `[int, float]`
        """
        if plotting_options is None:
            plotting_options = {
                "layout": {
                    "title_text": "Sex distribution in the samples",
                    "title_x": 0.5,
                },
                "xaxes": {"title_text": "sex"},
                "yaxes": {"title_text": "number of samples"},
                "traces": {"marker_color": ["pink", "blue"]},
            }
        else:
            plotting_options = add_default_titles_to_plotting_options(
                plotting_options,
                "Sex distribution in the samples",
                "sex",
                "number of samples",
            )
            plotting_options = add_x_to_plotting_options(
                plotting_options, "traces", "marker_color", ["pink", "blue"]
            )

        graph = BarGraph(
            pd.value_counts(self.metadata_df[sex_col]),
        )
        fig = graph.plot_one_graph(
            plotting_options=plotting_options,
            show=show,
            output_file=output_file,
        )

        return fig

    def plot_category_distribution(
        self,
        column_name,
        title=None,
        xlabel=None,
        reset_xnames_dic: dict = None,
        plotting_options: dict = None,
        show: Optional[bool] = True,
        output_file: Optional[str] = False,
    ):
        """
        :param column_name: name of the column you wish to display into a barplot
        :param title: title of the graph
        :param xlabel: label of the x axis
        :param reset_xnames_dic: to rename the names of the values in the x axis. \n
                                 Example for a plot of the distribution of smoking habits :
                                 reset_xnames_dic={'y': 'smoker', 'n': 'non smoker'}
        :param show: set to False if you don't want to show the plot
        :param output_file: name of the output file
        :param plotting_options: options of plotting that will override the default setup \n
                                 [!] Make sure the value given to an argument is of the right type \n
                                 options allowed : 'log': `bool` ; 'colorbar': `[str, List[str]]` ;
                                 'tickangle': `[int, float]`
        """
        if plotting_options is None:
            plotting_options = {
                "layout": {
                    "title_text": column_name + " distribution in the samples",
                    "title_x": 0.5,
                },
                "xaxes": {"title_text": column_name},
                "yaxes": {"title_text": "number of samples"},
            }
        else:
            plotting_options = add_default_titles_to_plotting_options(
                plotting_options,
                column_name + " distribution in the samples",
                column_name,
                "number of samples",
            )

        graph = BarGraph(
            pd.value_counts(self.metadata_df[column_name]),
        )
        # if reset_xnames_dic is not None:
        #     bar_fig.reset_xnames(reset_xnames_dic)
        fig = graph.plot_one_graph(
            plotting_options=plotting_options,
            show=show,
            output_file=output_file,
        )

        return fig