Coverage for biobb_ml/utils/correlation_matrix.py: 75%
75 statements
« prev ^ index » next coverage.py v7.5.1, created at 2024-05-07 09:39 +0000
« prev ^ index » next coverage.py v7.5.1, created at 2024-05-07 09:39 +0000
1#!/usr/bin/env python3
3"""Module containing the CorrelationMatrix class and the command line interface."""
4import argparse
5import pandas as pd
6import matplotlib.pyplot as plt
7import seaborn as sns
8from biobb_common.generic.biobb_object import BiobbObject
9from biobb_common.configuration import settings
10from biobb_common.tools import file_utils as fu
11from biobb_common.tools.file_utils import launchlogger
12from biobb_ml.utils.common import check_input_path, check_output_path, getHeader, getIndependentVars
15class CorrelationMatrix(BiobbObject):
16 """
17 | biobb_ml CorrelationMatrix
18 | Generates a correlation matrix from a given dataset.
20 Args:
21 input_dataset_path (str): Path to the input dataset. File type: input. `Sample file <https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/data/utils/dataset_correlation_matrix.csv>`_. Accepted formats: csv (edam:format_3752).
22 output_plot_path (str): Path to the correlation matrix plot. File type: output. `Sample file <https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/reference/utils/ref_output_plot_correlation_matrix.png>`_. Accepted formats: png (edam:format_3603).
23 properties (dic):
24 * **features** (*dict*) - ({}) Independent variables or columns from your dataset you want to compare. You can specify either a list of columns names from your input dataset, a list of columns indexes or a range of columns indexes. Formats: { "columns": ["column1", "column2"] } or { "indexes": [0, 2, 3, 10, 11, 17] } or { "range": [[0, 20], [50, 102]] }. In case of mulitple formats, the first one will be picked.
25 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
26 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
28 Examples:
29 This is a use example of how to use the building block from Python::
31 from biobb_ml.utils.correlation_matrix import correlation_matrix
32 prop = {
33 'features': {
34 'columns': [ 'column1', 'column2', 'column3' ]
35 }
36 }
37 correlation_matrix(input_dataset_path='/path/to/myDataset.csv',
38 output_plot_path='/path/to/newPlot.png',
39 properties=prop)
41 Info:
42 * wrapped_software:
43 * name: In house
44 * license: Apache-2.0
45 * ontology:
46 * name: EDAM
47 * schema: http://edamontology.org/EDAM.owl
49 """
51 def __init__(self, input_dataset_path, output_plot_path,
52 properties=None, **kwargs) -> None:
53 properties = properties or {}
55 # Call parent class constructor
56 super().__init__(properties)
57 self.locals_var_dict = locals().copy()
59 # Input/Output files
60 self.io_dict = {
61 "in": {"input_dataset_path": input_dataset_path},
62 "out": {"output_plot_path": output_plot_path}
63 }
65 # Properties specific for BB
66 self.features = properties.get('features', {})
67 self.properties = properties
69 # Check the properties
70 self.check_properties(properties)
71 self.check_arguments()
73 def check_data_params(self, out_log, err_log):
74 """ Checks all the input/output paths and parameters """
75 self.io_dict["in"]["input_dataset_path"] = check_input_path(self.io_dict["in"]["input_dataset_path"], "input_dataset_path", out_log, self.__class__.__name__)
76 self.io_dict["out"]["output_plot_path"] = check_output_path(self.io_dict["out"]["output_plot_path"], "output_plot_path", False, out_log, self.__class__.__name__)
78 @launchlogger
79 def launch(self) -> int:
80 """Execute the :class:`CorrelationMatrix <utils.correlation_matrix.CorrelationMatrix>` utils.correlation_matrix.CorrelationMatrix object."""
82 # check input/output paths and parameters
83 self.check_data_params(self.out_log, self.err_log)
85 # Setup Biobb
86 if self.check_restart():
87 return 0
88 self.stage_files()
90 # load dataset
91 fu.log('Getting dataset from %s' % self.io_dict["in"]["input_dataset_path"], self.out_log, self.global_log)
92 if 'columns' in self.features:
93 labels = getHeader(self.io_dict["in"]["input_dataset_path"])
94 skiprows = 1
95 else:
96 labels = None
97 skiprows = None
98 data = pd.read_csv(self.io_dict["in"]["input_dataset_path"], header=None, sep="\\s+|;|:|,|\t", engine="python", skiprows=skiprows, names=labels)
100 if self.features:
101 data = getIndependentVars(self.features, data, self.out_log, self.__class__.__name__)
103 fu.log('Parsing dataset', self.out_log, self.global_log)
104 if data.shape[1] < 10:
105 s = None
106 fs = 12
107 elif data.shape[1] >= 10 and data.shape[1] < 20:
108 s = (12, 12)
109 fs = 9
110 elif data.shape[1] >= 20:
111 s = (16, 16)
112 fs = 7
114 f, ax = plt.subplots(figsize=s)
115 corr = data.corr()
116 sns.heatmap(round(corr, 2), annot=True, ax=ax, cmap='Blues', fmt='.2f', square=True, annot_kws={"fontsize": fs})
117 f.subplots_adjust(top=0.93)
118 f.suptitle('Attributes Correlation Matrix', fontsize=14)
119 plt.tight_layout(rect=[0, 0.03, 1, 0.95])
121 plt.savefig(self.io_dict["out"]["output_plot_path"], dpi=150)
122 fu.log('Saving Correlation Matrix Plot to %s' % self.io_dict["out"]["output_plot_path"], self.out_log, self.global_log)
124 # Copy files to host
125 self.copy_to_host()
127 self.tmp_files.extend([
128 self.stage_io_dict.get("unique_dir")
129 ])
130 self.remove_tmp_files()
132 self.check_arguments(output_files_created=True, raise_exception=False)
134 return 0
137def correlation_matrix(input_dataset_path: str, output_plot_path: str, properties: dict = None, **kwargs) -> int:
138 """Execute the :class:`CorrelationMatrix <utils.correlation_matrix.CorrelationMatrix>` class and
139 execute the :meth:`launch() <utils.correlation_matrix.CorrelationMatrix.launch>` method."""
141 return CorrelationMatrix(input_dataset_path=input_dataset_path,
142 output_plot_path=output_plot_path,
143 properties=properties, **kwargs).launch()
146def main():
147 """Command line execution of this building block. Please check the command line documentation."""
148 parser = argparse.ArgumentParser(description="Generates a correlation matrix from a given dataset", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
149 parser.add_argument('--config', required=False, help='Configuration file')
151 # Specific args of each building block
152 required_args = parser.add_argument_group('required arguments')
153 required_args.add_argument('--input_dataset_path', required=True, help='Path to the input dataset. Accepted formats: csv.')
154 required_args.add_argument('--output_plot_path', required=True, help='Path to the correlation matrix plot. Accepted formats: png.')
156 args = parser.parse_args()
157 args.config = args.config or "{}"
158 properties = settings.ConfReader(config=args.config).get_prop_dic()
160 # Specific call of each building block
161 correlation_matrix(input_dataset_path=args.input_dataset_path,
162 output_plot_path=args.output_plot_path,
163 properties=properties)
166if __name__ == '__main__':
167 main()