Metadata-Version: 2.1
Name: hmap
Version: 0.9.1
Summary: A python package for heatmap clustering and plotting
Home-page: https://hmap.readthedocs.io/en/latest/index.html
Author: Matthias Bieg
Author-email: matthias.bieg@gmail.com
License: UNKNOWN
Description: **Author:** Matthias Bieg
        
        # hmap: Python Heatmap Package
        
        This package implements a convenient heatmap plotting package in python. It offers low level functions for
        
        1. Plotting
        	- Heatmaps
        	- Dendrograms
        	- Annotations
        	- Legends
        2. Figure layouting
        
        ## Clustered heatmap
        
        ![Clustered Heatmap](jupyter_notebooks/pics/clustered_heatmap.jpeg)
        
        ## Grouped clustered heatmap
        
        ![Grouped Clustered Heatmap](jupyter_notebooks/pics/grouped_clustered_heatmap.jpeg)
        
        ## Figure layout
        The hmap package comes with a module for defining the layout of a figure using absolute length measurements. Currently the only unit supported is milimeters. The layout of a figure is defined as a grid. You have to specify 
        - the number of rows, 
        - the number of columns, 
        - the widths of the columns,
        - the heights of the rows,
        - the vertical distance between adjacent rows, 
        - the horizontal distance between adjacent columns,
        - the size of the bottom border margin,
        - the size of the top border margin,
        - the size of the left border margin, and
        - the size of theright border margin
        As said before, the sizes are given in milimeters.
        
        ### Example
        
        ```python
        import sys
        import hmap
        import matplotlib.pyplot as plt
        
        fig, gs = hmap.layout.layout.layoutGrid(4, 5, [10., 2., 40., 40., 40], [10., 2., 40., 40.], 1., 1., 20., 15., 15., 20.)
        col_widths = ["10 mm", "2 mm", "40 mm", "40 mm", "40 mm"]
        row_heights = ["10 mm", "2 mm", "40 mm", "40 mm"]
        
        for row_idx in range(4):
            for col_idx in range(5):
                ax = plt.subplot(gs[row_idx, col_idx])
                plt.xticks([], [])
                plt.yticks([], [])
                if(row_idx == 0):
                    ax.xaxis.set_label_position("top")
                    plt.xlabel(col_widths[col_idx], 
                               fontsize=7, 
                               rotation=90)
                if(col_idx == 0):
                    plt.ylabel(row_heights[row_idx], 
                               fontsize=7, 
                               rotation=0, 
                               horizontalalignment="right",
                               verticalalignment="center")
        ```
        
        ![Figure layout](jupyter_notebooks/pics/figure_layout.jpeg)
        
        # Installation
        ```bash
        pip install hmap
        ```
        
        # Usage Example
        Please check the [jupyter notebook](jupyter_notebooks/hmap_example.ipynb) for an example of how to use hmap.
        
        # Acknowledgements
        This package was implemented during my time at the *German Cancer Research Center* in the group of *Theoretical Bioinformatics* headed by Prof. Dr. Roland Eils, where i was part of the core bioinformatics team of the *Heidelberg Institute of Personalized Oncology (HIPO)*. Further refinment and final upload to PyPI was done during my time at *Charite, Universitaetsmedizin Berlin, Berlin Institute of Health (BIH) in the Department of Digital Health* headed by Prof. Roland Eils.
        
        # License
        Copyright (c) 2021, Matthias Bieg
        
        Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.0
Description-Content-Type: text/markdown
