newdocs/API-analysis/cookbook-distance.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<h2><span style=\"color:gray\">ipyrad-analysis toolkit:</span> distance</h2>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Key features:\n",
    "\n",
    "1. Calculate pairwise genetic distances between samples. \n",
    "2. Filter SNPs to reduce missing data. \n",
    "3. Impute missing data using population allele frequencies."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### required software"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# conda install ipyrad -c bioconda\n",
    "# conda install toyplot -c eaton-lab (optional)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import ipyrad.analysis as ipa\n",
    "import toyplot"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Short tutorial"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Setup input files and params"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# the path to your VCF or HDF5 formatted snps file\n",
    "data = \"/home/deren/Downloads/ref_pop2.snps.hdf5\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# group individuals into populations\n",
    "imap = {\n",
    "    \"virg\": [\"TXWV2\", \"LALC2\", \"SCCU3\", \"FLSF33\", \"FLBA140\"],\n",
    "    \"mini\": [\"FLSF47\", \"FLMO62\", \"FLSA185\", \"FLCK216\"],\n",
    "    \"gemi\": [\"FLCK18\", \"FLSF54\", \"FLWO6\", \"FLAB109\"],\n",
    "    \"bran\": [\"BJSL25\", \"BJSB3\", \"BJVL19\"],\n",
    "    \"fusi\": [\"MXED8\", \"MXGT4\", \"TXGR3\", \"TXMD3\"],\n",
    "    \"sagr\": [\"CUVN10\", \"CUCA4\", \"CUSV6\", \"CUMM5\"],\n",
    "    \"oleo\": [\"CRL0030\", \"CRL0001\", \"HNDA09\", \"BZBB1\", \"MXSA3017\"],\n",
    "}\n",
    "\n",
    "# minimum n samples that must be present in each SNP from each group\n",
    "minmap = {i: 0.5 for i in imap}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### calculate distances"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Samples: 29\n",
      "Sites before filtering: 349914\n",
      "Filtered (indels): 0\n",
      "Filtered (bi-allel): 13379\n",
      "Filtered (mincov): 30459\n",
      "Filtered (minmap): 111825\n",
      "Filtered (combined): 120177\n",
      "Sites after filtering: 229737\n",
      "Sites containing missing values: 219551 (95.57%)\n",
      "Missing values in SNP matrix: 814369 (12.22%)\n",
      "Imputation: 'sampled'; (0, 1, 2) = 77.3%, 10.7%, 12.0%\n"
     ]
    }
   ],
   "source": [
    "# load the snp data into distance tool with arguments\n",
    "from ipyrad.analysis.distance import Distance\n",
    "dist = Distance(\n",
    "    data=data, \n",
    "    imap=imap,\n",
    "    minmap=minmap,\n",
    "    mincov=0.5,\n",
    "    impute_method=\"sample\",\n",
    "    subsample_snps=False,\n",
    ")\n",
    "dist.run()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### save results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# save to a CSV file\n",
    "dist.dists.to_csv(\"distances.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>BJSB3</th>\n",
       "      <th>BJSL25</th>\n",
       "      <th>BJVL19</th>\n",
       "      <th>BZBB1</th>\n",
       "      <th>CRL0001</th>\n",
       "      <th>CRL0030</th>\n",
       "      <th>CUCA4</th>\n",
       "      <th>CUMM5</th>\n",
       "      <th>CUSV6</th>\n",
       "      <th>CUVN10</th>\n",
       "      <th>...</th>\n",
       "      <th>FLWO6</th>\n",
       "      <th>HNDA09</th>\n",
       "      <th>LALC2</th>\n",
       "      <th>MXED8</th>\n",
       "      <th>MXGT4</th>\n",
       "      <th>MXSA3017</th>\n",
       "      <th>SCCU3</th>\n",
       "      <th>TXGR3</th>\n",
       "      <th>TXMD3</th>\n",
       "      <th>TXWV2</th>\n",
       "    </tr>\n",
       "  </thead>\n",
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       "      <td>...</td>\n",
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       "      <td>0.566156</td>\n",
       "      <td>0.559675</td>\n",
       "      <td>0.554665</td>\n",
       "      <td>0.542768</td>\n",
       "      <td>...</td>\n",
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       "      <td>0.457105</td>\n",
       "      <td>0.554882</td>\n",
       "    </tr>\n",
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       "      <th>BJVL19</th>\n",
       "      <td>0.253472</td>\n",
       "      <td>0.235900</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.567897</td>\n",
       "      <td>0.502775</td>\n",
       "      <td>0.547391</td>\n",
       "      <td>0.576355</td>\n",
       "      <td>0.569360</td>\n",
       "      <td>0.563000</td>\n",
       "      <td>0.554621</td>\n",
       "      <td>...</td>\n",
       "      <td>0.564728</td>\n",
       "      <td>0.555927</td>\n",
       "      <td>0.539913</td>\n",
       "      <td>0.441844</td>\n",
       "      <td>0.417060</td>\n",
       "      <td>0.556449</td>\n",
       "      <td>0.575336</td>\n",
       "      <td>0.464118</td>\n",
       "      <td>0.465476</td>\n",
       "      <td>0.562278</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>BZBB1</th>\n",
       "      <td>0.592255</td>\n",
       "      <td>0.558630</td>\n",
       "      <td>0.567897</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.280691</td>\n",
       "      <td>0.280569</td>\n",
       "      <td>0.422670</td>\n",
       "      <td>0.422962</td>\n",
       "      <td>0.426266</td>\n",
       "      <td>0.394242</td>\n",
       "      <td>...</td>\n",
       "      <td>0.559152</td>\n",
       "      <td>0.285883</td>\n",
       "      <td>0.532918</td>\n",
       "      <td>0.525701</td>\n",
       "      <td>0.542381</td>\n",
       "      <td>0.317450</td>\n",
       "      <td>0.576455</td>\n",
       "      <td>0.552554</td>\n",
       "      <td>0.551579</td>\n",
       "      <td>0.563571</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CRL0001</th>\n",
       "      <td>0.530145</td>\n",
       "      <td>0.494291</td>\n",
       "      <td>0.502775</td>\n",
       "      <td>0.280691</td>\n",
       "      <td>0.000000</td>\n",
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       "      <td>0.322277</td>\n",
       "      <td>0.342836</td>\n",
       "      <td>0.213266</td>\n",
       "      <td>...</td>\n",
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       "      <td>0.262217</td>\n",
       "      <td>0.451717</td>\n",
       "      <td>0.466429</td>\n",
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       "      <td>0.484123</td>\n",
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       "            BJSB3    BJSL25    BJVL19     BZBB1   CRL0001   CRL0030     CUCA4  \\\n",
       "BJSB3    0.000000  0.250447  0.253472  0.592255  0.530145  0.572576  0.601853   \n",
       "BJSL25   0.250447  0.000000  0.235900  0.558630  0.494291  0.537193  0.566156   \n",
       "BJVL19   0.253472  0.235900  0.000000  0.567897  0.502775  0.547391  0.576355   \n",
       "BZBB1    0.592255  0.558630  0.567897  0.000000  0.280691  0.280569  0.422670   \n",
       "CRL0001  0.530145  0.494291  0.502775  0.280691  0.000000  0.239596  0.347859   \n",
       "\n",
       "            CUMM5     CUSV6    CUVN10  ...     FLWO6    HNDA09     LALC2  \\\n",
       "BJSB3    0.597044  0.591990  0.579937  ...  0.594005  0.582000  0.568137   \n",
       "BJSL25   0.559675  0.554665  0.542768  ...  0.558769  0.548897  0.532239   \n",
       "BJVL19   0.569360  0.563000  0.554621  ...  0.564728  0.555927  0.539913   \n",
       "BZBB1    0.422962  0.426266  0.394242  ...  0.559152  0.285883  0.532918   \n",
       "CRL0001  0.322277  0.342836  0.213266  ...  0.470064  0.262217  0.451717   \n",
       "\n",
       "            MXED8     MXGT4  MXSA3017     SCCU3     TXGR3     TXMD3     TXWV2  \n",
       "BJSB3    0.464618  0.443942  0.579789  0.603638  0.487945  0.487936  0.590440  \n",
       "BJSL25   0.435050  0.412694  0.547182  0.567323  0.453606  0.457105  0.554882  \n",
       "BJVL19   0.441844  0.417060  0.556449  0.575336  0.464118  0.465476  0.562278  \n",
       "BZBB1    0.525701  0.542381  0.317450  0.576455  0.552554  0.551579  0.563571  \n",
       "CRL0001  0.466429  0.477764  0.299538  0.492224  0.487327  0.484123  0.482726  \n",
       "\n",
       "[5 rows x 29 columns]"
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     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "# show the upper corner \n",
    "dist.dists.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Draw the matrix"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
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       "{\n",
       "var modules={};\n",
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       "    {\n",
       "        var tables = [];\n",
       "\n",
       "        var module = {};\n",
       "\n",
       "        module.set = function(owner, key, names, columns)\n",
       "        {\n",
       "            tables.push({owner: owner, key: key, names: names, columns: columns});\n",
       "        }\n",
       "\n",
       "        module.get = function(owner, key)\n",
       "        {\n",
       "            for(var i = 0; i != tables.length; ++i)\n",
       "            {\n",
       "                var table = tables[i];\n",
       "                if(table.owner != owner)\n",
       "                    continue;\n",
       "                if(table.key != key)\n",
       "                    continue;\n",
       "                return {names: table.names, columns: table.columns};\n",
       "            }\n",
       "        }\n",
       "\n",
       "        module.get_csv = function(owner, key)\n",
       "        {\n",
       "            var table = module.get(owner, key);\n",
       "            if(table != undefined)\n",
       "            {\n",
       "                var csv = \"\";\n",
       "                csv += table.names.join(\",\") + \"\\n\";\n",
       "                for(var i = 0; i != table.columns[0].length; ++i)\n",
       "                {\n",
       "                  for(var j = 0; j != table.columns.length; ++j)\n",
       "                  {\n",
       "                    if(j)\n",
       "                      csv += \",\";\n",
       "                    csv += table.columns[j][i];\n",
       "                  }\n",
       "                  csv += \"\\n\";\n",
       "                }\n",
       "                return csv;\n",
       "            }\n",
       "        }\n",
       "\n",
       "        return module;\n",
       "    })();\n",
       "modules[\"toyplot/root/id\"] = \"t8c90f8d8c36449b0ac268cb2c5e595de\";\n",
       "modules[\"toyplot/root\"] = (function(root_id)\n",
       "    {\n",
       "        return document.querySelector(\"#\" + root_id);\n",
       "    })(modules[\"toyplot/root/id\"]);\n",
       "modules[\"toyplot/canvas/id\"] = \"td59966f185b849fa9dae639ce90d3bbf\";\n",
       "modules[\"toyplot/canvas\"] = (function(canvas_id)\n",
       "    {\n",
       "        return document.querySelector(\"#\" + canvas_id);\n",
       "    })(modules[\"toyplot/canvas/id\"]);\n",
       "modules[\"toyplot/menus/context\"] = (function(root, canvas)\n",
       "    {\n",
       "        var wrapper = document.createElement(\"div\");\n",
       "        wrapper.innerHTML = \"<ul class='toyplot-context-menu' style='background:#eee; border:1px solid #b8b8b8; border-radius:5px; box-shadow: 0px 0px 8px rgba(0%,0%,0%,0.25); margin:0; padding:3px 0; position:fixed; visibility:hidden;'></ul>\"\n",
       "        var menu = wrapper.firstChild;\n",
       "\n",
       "        root.appendChild(menu);\n",
       "\n",
       "        var items = [];\n",
       "\n",
       "        var ignore_mouseup = null;\n",
       "        function open_menu(e)\n",
       "        {\n",
       "            var show_menu = false;\n",
       "            for(var index=0; index != items.length; ++index)\n",
       "            {\n",
       "                var item = items[index];\n",
       "                if(item.show(e))\n",
       "                {\n",
       "                    item.item.style.display = \"block\";\n",
       "                    show_menu = true;\n",
       "                }\n",
       "                else\n",
       "                {\n",
       "                    item.item.style.display = \"none\";\n",
       "                }\n",
       "            }\n",
       "\n",
       "            if(show_menu)\n",
       "            {\n",
       "                ignore_mouseup = true;\n",
       "                menu.style.left = (e.clientX + 1) + \"px\";\n",
       "                menu.style.top = (e.clientY - 5) + \"px\";\n",
       "                menu.style.visibility = \"visible\";\n",
       "                e.stopPropagation();\n",
       "                e.preventDefault();\n",
       "            }\n",
       "        }\n",
       "\n",
       "        function close_menu()\n",
       "        {\n",
       "            menu.style.visibility = \"hidden\";\n",
       "        }\n",
       "\n",
       "        function contextmenu(e)\n",
       "        {\n",
       "            open_menu(e);\n",
       "        }\n",
       "\n",
       "        function mousemove(e)\n",
       "        {\n",
       "            ignore_mouseup = false;\n",
       "        }\n",
       "\n",
       "        function mouseup(e)\n",
       "        {\n",
       "            if(ignore_mouseup)\n",
       "            {\n",
       "                ignore_mouseup = false;\n",
       "                return;\n",
       "            }\n",
       "            close_menu();\n",
       "        }\n",
       "\n",
       "        function keydown(e)\n",
       "        {\n",
       "            if(e.key == \"Escape\" || e.key == \"Esc\" || e.keyCode == 27)\n",
       "            {\n",
       "                close_menu();\n",
       "            }\n",
       "        }\n",
       "\n",
       "        canvas.addEventListener(\"contextmenu\", contextmenu);\n",
       "        canvas.addEventListener(\"mousemove\", mousemove);\n",
       "        document.addEventListener(\"mouseup\", mouseup);\n",
       "        document.addEventListener(\"keydown\", keydown);\n",
       "\n",
       "        var module = {};\n",
       "        module.add_item = function(label, show, activate)\n",
       "        {\n",
       "            var wrapper = document.createElement(\"div\");\n",
       "            wrapper.innerHTML = \"<li class='toyplot-context-menu-item' style='background:#eee; color:#333; padding:2px 20px; list-style:none; margin:0; text-align:left;'>\" + label + \"</li>\"\n",
       "            var item = wrapper.firstChild;\n",
       "\n",
       "            items.push({item: item, show: show});\n",
       "\n",
       "            function mouseover()\n",
       "            {\n",
       "                this.style.background = \"steelblue\";\n",
       "                this.style.color = \"white\";\n",
       "            }\n",
       "\n",
       "            function mouseout()\n",
       "            {\n",
       "                this.style.background = \"#eee\";\n",
       "                this.style.color = \"#333\";\n",
       "            }\n",
       "\n",
       "            function choose_item(e)\n",
       "            {\n",
       "                close_menu();\n",
       "                activate();\n",
       "\n",
       "                e.stopPropagation();\n",
       "                e.preventDefault();\n",
       "            }\n",
       "\n",
       "            item.addEventListener(\"mouseover\", mouseover);\n",
       "            item.addEventListener(\"mouseout\", mouseout);\n",
       "            item.addEventListener(\"mouseup\", choose_item);\n",
       "            item.addEventListener(\"contextmenu\", choose_item);\n",
       "\n",
       "            menu.appendChild(item);\n",
       "        };\n",
       "        return module;\n",
       "    })(modules[\"toyplot/root\"],modules[\"toyplot/canvas\"]);\n",
       "modules[\"toyplot/io\"] = (function()\n",
       "    {\n",
       "        var module = {};\n",
       "        module.save_file = function(mime_type, charset, data, filename)\n",
       "        {\n",
       "            var uri = \"data:\" + mime_type + \";charset=\" + charset + \",\" + data;\n",
       "            uri = encodeURI(uri);\n",
       "\n",
       "            var link = document.createElement(\"a\");\n",
       "            if(typeof link.download != \"undefined\")\n",
       "            {\n",
       "              link.href = uri;\n",
       "              link.style = \"visibility:hidden\";\n",
       "              link.download = filename;\n",
       "\n",
       "              document.body.appendChild(link);\n",
       "              link.click();\n",
       "              document.body.removeChild(link);\n",
       "            }\n",
       "            else\n",
       "            {\n",
       "              window.open(uri);\n",
       "            }\n",
       "        };\n",
       "        return module;\n",
       "    })();\n",
       "(function(tables, context_menu, io, owner_id, key, label, names, columns, filename)\n",
       "        {\n",
       "            tables.set(owner_id, key, names, columns);\n",
       "\n",
       "            var owner = document.querySelector(\"#\" + owner_id);\n",
       "            function show_item(e)\n",
       "            {\n",
       "                return owner.contains(e.target);\n",
       "            }\n",
       "\n",
       "            function choose_item()\n",
       "            {\n",
       "                io.save_file(\"text/csv\", \"utf-8\", tables.get_csv(owner_id, key), filename + \".csv\");\n",
       "            }\n",
       "\n",
       "            context_menu.add_item(\"Save \" + label + \" as CSV\", show_item, choose_item);\n",
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       "})();</script></div></div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "toyplot.matrix(\n",
    "    dist.dists, \n",
    "    bshow=False,\n",
    "    tshow=False,\n",
    "    rlocator=toyplot.locator.Explicit(\n",
    "        range(len(dist.names)),\n",
    "        sorted(dist.names),\n",
    "));"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Draw matrix reordered to match groups in imap"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "# get list of concatenated names from each group\n",
    "ordered_names = []\n",
    "for group in dist.imap.values():\n",
    "    ordered_names += group\n",
    "\n",
    "# reorder matrix to match name order    \n",
    "ordered_matrix = dist.dists[ordered_names].T[ordered_names]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
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       "{\n",
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       "                var csv = \"\";\n",
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       "        var module = {};\n",
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       "\n",
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       "        };\n",
       "        return module;\n",
       "    })(modules[\"toyplot/root\"],modules[\"toyplot/canvas\"]);\n",
       "modules[\"toyplot/io\"] = (function()\n",
       "    {\n",
       "        var module = {};\n",
       "        module.save_file = function(mime_type, charset, data, filename)\n",
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       "            {\n",
       "              window.open(uri);\n",
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       "        return module;\n",
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       "            {\n",
       "                io.save_file(\"text/csv\", \"utf-8\", tables.get_csv(owner_id, key), filename + \".csv\");\n",
       "            }\n",
       "\n",
       "            context_menu.add_item(\"Save \" + label + \" as CSV\", show_item, choose_item);\n",
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       "})();</script></div></div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "toyplot.matrix(\n",
    "    ordered_matrix,\n",
    "    bshow=False,\n",
    "    tshow=False,\n",
    "    rlocator=toyplot.locator.Explicit(\n",
    "        range(len(ordered_names)),\n",
    "        ordered_names,\n",
    "));"
   ]
  }
 ],
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