{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "%matplotlib inline" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Enrichment Plot" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "A function to plot step plots of cumulative counts." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "> from mlxtend.general_plotting import category_scatter" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Overview" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In enrichment plots, the y-axis can be interpreted as \"how many samples are less or equal to the corresponding x-axis label.\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### References\n", "\n", "- -" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Example 1 - Enrichment Plots from Pandas DataFrames" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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" ], "text/plain": [ " X1 X2\n", "0 1.1 1.5\n", "1 2.1 1.8\n", "2 3.1 2.1\n", "3 3.9 2.5" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import pandas as pd\n", "s1 = [1.1, 1.5]\n", "s2 = [2.1, 1.8]\n", "s3 = [3.1, 2.1]\n", "s4 = [3.9, 2.5]\n", "data = [s1, s2, s3, s4]\n", "df = pd.DataFrame(data, columns=['X1', 'X2'])\n", "df" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Plotting the data where the categories are determined by the unique values in the label column `label_col`. The `x` and `y` values are simply the column names of the DataFrame that we want to plot." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "image/png": 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"text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import matplotlib.pyplot as plt\n", "from mlxtend.plotting import enrichment_plot\n", "\n", "ax = enrichment_plot(df, legend_loc='upper left')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## API" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "## enrichment_plot\n", "\n", "*enrichment_plot(df, colors='bgrkcy', markers=' ', linestyles='-', alpha=0.5, lw=2, where='post', grid=True, count_label='Count', xlim='auto', ylim='auto', invert_axes=False, legend_loc='best', ax=None)*\n", "\n", "Plot stacked barplots\n", "\n", "**Parameters**\n", "\n", "- `df` : pandas.DataFrame\n", "\n", " A pandas DataFrame where columns represent the different categories.\n", " colors: str (default: 'bgrcky')\n", " The colors of the bars.\n", "\n", "- `markers` : str (default: ' ')\n", "\n", " Matplotlib markerstyles, e.g,\n", " 'sov' for square,circle, and triangle markers.\n", "\n", "- `linestyles` : str (default: '-')\n", "\n", " Matplotlib linestyles, e.g.,\n", " '-,--' to cycle normal and dashed lines. Note\n", " that the different linestyles need to be separated by commas.\n", "\n", "- `alpha` : float (default: 0.5)\n", "\n", " Transparency level from 0.0 to 1.0.\n", "\n", "- `lw` : int or float (default: 2)\n", "\n", " Linewidth parameter.\n", "\n", "- `where` : {'post', 'pre', 'mid'} (default: 'post')\n", "\n", " Starting location of the steps.\n", "\n", "- `grid` : bool (default: `True`)\n", "\n", " Plots a grid if True.\n", "\n", "- `count_label` : str (default: 'Count')\n", "\n", " Label for the \"Count\"-axis.\n", "\n", "- `xlim` : 'auto' or array-like [min, max] (default: 'auto')\n", "\n", " Min and maximum position of the x-axis range.\n", "\n", "- `ylim` : 'auto' or array-like [min, max] (default: 'auto')\n", "\n", " Min and maximum position of the y-axis range.\n", "\n", "- `invert_axes` : bool (default: False)\n", "\n", " Plots count on the x-axis if True.\n", "\n", "- `legend_loc` : str (default: 'best')\n", "\n", " Location of the plot legend\n", " {best, upper left, upper right, lower left, lower right}\n", " No legend if legend_loc=False\n", "\n", "- `ax` : matplotlib axis, optional (default: None)\n", "\n", " Use this axis for plotting or make a new one otherwise\n", "\n", "**Returns**\n", "\n", "- `ax` : matplotlib axis\n", "\n", "\n", "**Examples**\n", "\n", "For usage examples, please see\n", " [http://rasbt.github.io/mlxtend/user_guide/plotting/enrichment_plot/](http://rasbt.github.io/mlxtend/user_guide/plotting/enrichment_plot/)\n", "\n", "\n" ] } ], "source": [ "with open('../../api_modules/mlxtend.plotting/enrichment_plot.md', 'r') as f:\n", " print(f.read())" ] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.4" }, "toc": { "nav_menu": {}, "number_sections": true, "sideBar": true, "skip_h1_title": false, "title_cell": "Table of Contents", "title_sidebar": "Contents", "toc_cell": false, "toc_position": {}, "toc_section_display": true, "toc_window_display": false } }, "nbformat": 4, "nbformat_minor": 1 }