Exercise4_6WalkthroughMPL.ipynb 7.02 KB
 Toby Hodges committed Jan 05, 2016 1 2 ``````{ "cells": [ `````` Toby Hodges committed Mar 30, 2016 3 4 5 6 7 8 9 10 11 12 13 14 15 16 `````` { "cell_type": "markdown", "metadata": {}, "source": [ "# Introduction to Python Programming" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Walkthrough: Exercise 4.6 - Plotting with `matplotlib`" ] }, `````` Toby Hodges committed Jan 05, 2016 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 `````` { "cell_type": "markdown", "metadata": { "collapsed": false, "slideshow": { "slide_type": "slide" } }, "source": [ "This notebook runs briefly through a solution to the exercise at the end of Worksheet 4 of the _Introduction to Python Programming_ course workbook." ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "subslide" } }, "source": [ "Start by importing the additional functionality that you need, to print the data structure and draw the plots." ] }, { "cell_type": "code", `````` Toby Hodges committed Mar 29, 2016 42 `````` "execution_count": null, `````` Toby Hodges committed Jan 05, 2016 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 `````` "metadata": { "collapsed": false, "slideshow": { "slide_type": "-" } }, "outputs": [], "source": [ "import pprint\n", "import matplotlib.pyplot as plt\n", "\n", "# the next line is for plotting in the IPython notebook only\n", "%matplotlib inline" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Now define the function that will draw each barchart of observations. (This function definition contains a list of colors for the bars, as tuples of RGB values, that will plot each species in a different color.)" ] }, { "cell_type": "code", `````` Toby Hodges committed Mar 29, 2016 71 `````` "execution_count": null, `````` Toby Hodges committed Jan 05, 2016 72 73 74 75 76 77 78 79 80 81 `````` "metadata": { "collapsed": true, "slideshow": { "slide_type": "subslide" } }, "outputs": [], "source": [ "def doBarChart(heights, labels, title, rows, columns, subplot):\n", " plt.subplot(rows, columns, subplot)\n", `````` Toby Hodges committed Mar 17, 2016 82 `````` " plt.bar(range(len(labels)), heights)#, color=[(0.9,0.05,0.05),(0.35,1.0,0.35),(0.05,0.05,0.9),(0.9,1.0,0.0),(0.7,0.1,0.7),(0.05,0.9,0.05),(1.0,0.5,0.5),(0.0,0.0,0.5),(0.75,0.75,0.0),(0.0,0.3,0.3),(0.0,0.5,0.0),(0.2,0.8,0.8),(0.6,0.05,0.25)])\n", `````` Toby Hodges committed Jan 05, 2016 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 `````` " plt.title(title)\n", " plt.xlabel('Taxon')\n", " plt.ylabel('Abundance')\n", " plt.axis([0, len(labels), 0, 25000])\n", " tickPos = []\n", " for pos in range(len(labels)):\n", " tickPos.append(pos+0.4)\n", " plt.xticks(tickPos,labels)" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Initialise an empty dictionary, to store the data for each site, and an empty list, to store the species names as you find them. Then, open a file object and read the data line-by-line, populating the data structures as you go." ] }, { "cell_type": "code", `````` Toby Hodges committed Mar 29, 2016 106 `````` "execution_count": null, `````` Toby Hodges committed Jan 05, 2016 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 `````` "metadata": { "collapsed": false, "slideshow": { "slide_type": "subslide" } }, "outputs": [], "source": [ "sites = {}\n", "taxa = []\n", "# make sure that you change the file path below to specify the location of the data file on your system\n", "datafile = open('speciesDistribution.txt', 'r')\n", "\n", "for line in datafile:\n", " line = line.strip()\n", " if line.startswith('Site:'):\n", " tag, siteName = line.split(\" \", 1)\n", " sites[siteName] = {}\n", " else:\n", " taxonID, count = line.split()\n", " count = int(count)\n", " sites[siteName][taxonID] = count\n", " if taxonID not in taxa:\n", " taxa.append(taxonID)" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ `````` Toby Hodges committed Mar 30, 2016 141 `````` "Now that you have read all of the data from the file, you need to loop over each site again, to add zero values for each species not observed. (Exercise 4.4)" `````` Toby Hodges committed Jan 05, 2016 142 143 144 145 `````` ] }, { "cell_type": "code", `````` Toby Hodges committed Mar 29, 2016 146 `````` "execution_count": null, `````` Toby Hodges committed Jan 05, 2016 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 `````` "metadata": { "collapsed": true, "slideshow": { "slide_type": "subslide" } }, "outputs": [], "source": [ "for site in sites:\n", " for taxon in taxa:\n", " if taxon not in sites[site]:\n", " sites[site][taxon] = 0" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ `````` Toby Hodges committed Mar 30, 2016 169 `````` "Now, you should have a dictionary, `sites`, keyed by site names, with values that are themselves dictionaries keyed by species ID. Each of these dictionaries within `sites` should have the same number of entries because you added the zero counts. To check out the overall data structure, you can use `pprint.PrettyPrinter`. (Exercise 4.5)" `````` Toby Hodges committed Jan 05, 2016 170 171 172 173 `````` ] }, { "cell_type": "code", `````` Toby Hodges committed Mar 29, 2016 174 `````` "execution_count": null, `````` Toby Hodges committed Jan 05, 2016 175 176 177 178 179 180 `````` "metadata": { "collapsed": false, "slideshow": { "slide_type": "subslide" } }, `````` Toby Hodges committed Mar 29, 2016 181 `````` "outputs": [], `````` Toby Hodges committed Jan 05, 2016 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 `````` "source": [ "pp = pprint.PrettyPrinter(indent=4)\n", "pp.pprint(sites)" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Looks good to me! Now, you want to be able to control the order in which the species and counts are extracted from this dictionary for plotting. To do this, you use the dictionary keys and the list of species names that were compiled when the data was read from the file. To make the plot more intuitive, you can make sure that both of these are sorted alphabetically." ] }, { "cell_type": "code", `````` Toby Hodges committed Mar 29, 2016 200 `````` "execution_count": null, `````` Toby Hodges committed Jan 05, 2016 201 202 203 204 205 206 `````` "metadata": { "collapsed": false, "slideshow": { "slide_type": "fragment" } }, `````` Toby Hodges committed Mar 04, 2016 207 `````` "outputs": [], `````` Toby Hodges committed Jan 05, 2016 208 `````` "source": [ `````` Toby Hodges committed Mar 17, 2016 209 `````` "taxa.sort()\n", `````` Toby Hodges committed Jan 05, 2016 210 `````` "siteNames = sites.keys()\n", `````` Toby Hodges committed Mar 17, 2016 211 `````` "siteNames = sorted(siteNames)" `````` Toby Hodges committed Jan 05, 2016 212 213 214 215 216 217 218 219 220 221 `````` ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "skip" } }, "source": [ `````` Toby Hodges committed Mar 30, 2016 222 `````` "Now, you are ready to plot the data using the function defined above. (Exercise 4.6)" `````` Toby Hodges committed Jan 05, 2016 223 224 225 226 `````` ] }, { "cell_type": "code", `````` Toby Hodges committed Mar 29, 2016 227 `````` "execution_count": null, `````` Toby Hodges committed Jan 05, 2016 228 229 230 231 232 233 `````` "metadata": { "collapsed": false, "slideshow": { "slide_type": "slide" } }, `````` Toby Hodges committed Mar 29, 2016 234 `````` "outputs": [], `````` Toby Hodges committed Jan 05, 2016 235 236 237 238 239 240 241 242 243 `````` "source": [ "plt.figure(1, figsize=(10,10)) # you can choose your own figure size or leave\n", " # this argument out to use the default setting.\n", "\n", "subnumber = 0\n", "\n", "for site in siteNames:\n", " subnumber += 1\n", " barValues = []\n", `````` Toby Hodges committed Mar 17, 2016 244 245 246 `````` " for taxon in taxa:\n", " barValues.append(sites[site][taxon])\n", " doBarChart(barValues, taxa, site, 4, 2, subnumber)\n", `````` Toby Hodges committed Jan 05, 2016 247 248 249 250 251 252 253 254 `````` "\n", "plt.tight_layout()\n", "plt.show()" ] } ], "metadata": { "kernelspec": { `````` Toby Hodges committed Mar 04, 2016 255 `````` "display_name": "Python 3", `````` Toby Hodges committed Jan 05, 2016 256 `````` "language": "python", `````` Toby Hodges committed Mar 04, 2016 257 `````` "name": "python3" `````` Toby Hodges committed Jan 05, 2016 258 259 260 261 `````` }, "language_info": { "codemirror_mode": { "name": "ipython", `````` Toby Hodges committed Mar 04, 2016 262 `````` "version": 3 `````` Toby Hodges committed Jan 05, 2016 263 264 265 266 267 `````` }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", `````` Toby Hodges committed Mar 04, 2016 268 269 `````` "pygments_lexer": "ipython3", "version": "3.5.1" `````` Toby Hodges committed Jan 05, 2016 270 271 272 273 274 `````` } }, "nbformat": 4, "nbformat_minor": 0 }``````