Source code for immuneML.analysis.data_manipulation.DataReshaper

import copy

import pandas as pd
from scipy.sparse import issparse

from immuneML.data_model.datasets.Dataset import Dataset




class DataReshaper:



    @staticmethod
    def reshape(dataset: Dataset, labels=None):
        """
        Takes a 2D matrix of values from the encoded data and reshapes it to long format,
        retaining the column and row annotations. This is for ease of use in plotting the data.
        It is suggested that some sort of filtering is done first, otherwise the memory usage may explode, as
        the resulting data frame is of shape
        (matrix.shape[0] * matrix.shape[1], labels.shape[0] + feature_annotations.shape[1] + 1)
        """
        if labels is None:
            row_annotations = pd.DataFrame(dataset.encoded_data.labels)
        else:
            row_annotations = pd.DataFrame(dataset.get_metadata(labels, return_df=True))

        row_annotations["example_id"] = dataset.encoded_data.example_ids

        if dataset.encoded_data.feature_annotations is not None:
            column_annotations = copy.deepcopy(dataset.encoded_data.feature_annotations)
            column_annotations["feature"] = dataset.encoded_data.feature_names
        else:
            column_annotations = pd.DataFrame({'feature': dataset.encoded_data.feature_names})

        matrix = dataset.encoded_data.examples
        matrix_1d = matrix.A.ravel() if issparse(matrix) else matrix.ravel()

        column_annotations = pd.concat([column_annotations]*matrix.shape[0], ignore_index=True)
        row_annotations = pd.DataFrame(row_annotations.values.repeat(matrix.shape[1], axis=0), columns=row_annotations.columns)
        data = pd.concat([row_annotations.reset_index(drop=True), column_annotations.reset_index(drop=True), pd.DataFrame({"value": matrix_1d})], axis=1)

        for column in data.columns:
            data[column] = pd.to_numeric(data[column], errors="ignore")

        return data