rare_snps.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {},
   "outputs": [],
   "source": [
    "library(SummarizedExperiment)\n",
    "library(VariantAnnotation)\n",
    "library(Rtsne)\n",
    "library(ggplot2)\n",
    "library(gplots)\n",
    "library(dplyr)\n",
    "library(irlba)\n",
    "library(umap)\n",
    "library(igraph)\n",
    "library(FNN)\n",
    "vcf <- readRDS('~/Dropbox/mixed/original/Map_K10_VBC_CLI.whitelist.noindel.rds')\n",
    "meta <- read.csv('~/Dropbox/mixed/meta/MetaDATAJohnes2.csv', header = TRUE)\n",
    "rownames(meta) <- meta$SeqID\n",
    "meta <- meta[colnames(vcf), ]\n",
    "meta <- meta %>% mutate(Farms = sprintf('farm_%d', Farm))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "GT <- geno(vcf)$GT"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\n",
       "      .     0/0     0/1     0/2     0/3     1/1 \n",
       "    346 1434753    5506     199       9    5562 "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "\n",
       "    0/0     0/1     1/1 \n",
       "1435099    5714    5562 "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "table(c(GT))\n",
    "GT[GT %in% c('.')] <- '0/0' # missing values\n",
    "GT[GT%in% c('0/2', '0/3')] <- '0/1'\n",
    "table(c(GT))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [],
   "source": [
    "# We define the orphan snps as the ones that are present in only one sample as\n",
    "# heterozygous or homozygous SNP\n",
    "GT_freq <- do.call('rbind', lapply(\n",
    "    1:nrow(GT), \n",
    "    function(i) GT[i, ] %>% factor(c('0/0', '0/1', '1/1'), labels = c('AA', 'AB', 'BB')) %>% table()\n",
    ")) %>% \n",
    "    as.data.frame() %>%\n",
    "    mutate(snp_id = rownames(GT)) %>%\n",
    "    filter(BB > 1 & AA > 1) %>% \n",
    "    arrange(BB)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 102,
   "metadata": {},
   "outputs": [],
   "source": [
    "states <- c('MN','NY', 'PA', 'VT')\n",
    "GT_AB_states <- do.call('rbind', lapply(1:nrow(GT_freq), function(i){\n",
    "    j <- GT[GT_freq[i, 'snp_id'], ] %in% c('0/1') \n",
    "    (meta$State[j] %>% factor(states) %>% table()) \n",
    "})) \n",
    "colnames(GT_AB_states) <- sprintf('%s_AB', colnames(GT_AB_states))\n",
    "GT_BB_states <- do.call('rbind', lapply(1:nrow(GT_freq), function(i){\n",
    "    j <- GT[GT_freq[i, 'snp_id'], ] %in% c('1/1') \n",
    "    (meta$State[j] %>% factor(states) %>% table()) \n",
    "})) \n",
    "colnames(GT_BB_states) <- sprintf('%s_BB', colnames(GT_BB_states))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 103,
   "metadata": {},
   "outputs": [],
   "source": [
    "df <- cbind(GT_freq, GT_AB_states, GT_BB_states)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 105,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>AA</th><th scope=col>AB</th><th scope=col>BB</th><th scope=col>snp_id</th><th scope=col>MN_AB</th><th scope=col>NY_AB</th><th scope=col>PA_AB</th><th scope=col>VT_AB</th><th scope=col>MN_BB</th><th scope=col>NY_BB</th><th scope=col>PA_BB</th><th scope=col>VT_BB</th></tr></thead>\n",
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       "\t<tr><td>465                        </td><td> 6                         </td><td> 54                        </td><td>Map_K10_VBC_CLI:2151370_C/G</td><td>5                          </td><td> 1                         </td><td>0                          </td><td>0                          </td><td>14                         </td><td> 13                        </td><td>21                         </td><td>  6                        </td></tr>\n",
       "\t<tr><td>465                        </td><td> 6                         </td><td> 54                        </td><td>Map_K10_VBC_CLI:2167917_C/T</td><td>5                          </td><td> 1                         </td><td>0                          </td><td>0                          </td><td>14                         </td><td> 13                        </td><td>21                         </td><td>  6                        </td></tr>\n",
       "\t<tr><td>193                        </td><td> 6                         </td><td>326                        </td><td>Map_K10_VBC_CLI:76286_G/T  </td><td>0                          </td><td> 6                         </td><td>0                          </td><td>0                          </td><td> 0                         </td><td>146                        </td><td> 4                         </td><td>176                        </td></tr>\n",
       "\t<tr><td>516                        </td><td> 7                         </td><td>  2                        </td><td>Map_K10_VBC_CLI:38870_A/G  </td><td>0                          </td><td> 7                         </td><td>0                          </td><td>0                          </td><td> 0                         </td><td>  2                        </td><td> 0                         </td><td>  0                        </td></tr>\n",
       "\t<tr><td>515                        </td><td> 7                         </td><td>  3                        </td><td>Map_K10_VBC_CLI:138160_G/A </td><td>0                          </td><td> 7                         </td><td>0                          </td><td>0                          </td><td> 0                         </td><td>  3                        </td><td> 0                         </td><td>  0                        </td></tr>\n",
       "\t<tr><td>514                        </td><td> 8                         </td><td>  3                        </td><td>Map_K10_VBC_CLI:5726_C/T   </td><td>0                          </td><td> 8                         </td><td>0                          </td><td>0                          </td><td> 0                         </td><td>  3                        </td><td> 0                         </td><td>  0                        </td></tr>\n",
       "\t<tr><td>441                        </td><td>12                         </td><td> 72                        </td><td>Map_K10_VBC_CLI:2168916_C/T</td><td>0                          </td><td>12                         </td><td>0                          </td><td>0                          </td><td> 0                         </td><td> 67                        </td><td> 3                         </td><td>  2                        </td></tr>\n",
       "\t<tr><td>478                        </td><td>14                         </td><td> 33                        </td><td>Map_K10_VBC_CLI:2126897_A/C</td><td>0                          </td><td>14                         </td><td>0                          </td><td>0                          </td><td> 0                         </td><td> 33                        </td><td> 0                         </td><td>  0                        </td></tr>\n",
       "\t<tr><td>458                        </td><td>15                         </td><td> 52                        </td><td>Map_K10_VBC_CLI:182378_G/A </td><td>0                          </td><td>15                         </td><td>0                          </td><td>0                          </td><td> 0                         </td><td> 52                        </td><td> 0                         </td><td>  0                        </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllllllllll}\n",
       " AA & AB & BB & snp\\_id & MN\\_AB & NY\\_AB & PA\\_AB & VT\\_AB & MN\\_BB & NY\\_BB & PA\\_BB & VT\\_BB\\\\\n",
       "\\hline\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:6008\\_C/T    & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:9890\\_C/T    & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:10583\\_G/A   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:28335\\_G/A   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:49215\\_A/G   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:71631\\_G/A   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:77046\\_G/T   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:120560\\_C/T  & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:122449\\_C/T  & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:157436\\_G/T  & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:164089\\_C/T  & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:175227\\_A/G  & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:2009251\\_G/A & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:2040397\\_G/C & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:2046193\\_C/T & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:4015985\\_G/A & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:4028613\\_G/A & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:4038386\\_G/A & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:4044695\\_G/A & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 1                                   & 1                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:4072026\\_C/T & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:4088155\\_G/A & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:4111125\\_G/A & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                  \\\\\n",
       "\t 523                                 & 0                                   & 2                                   & Map\\_K10\\_VBC\\_CLI:4113491\\_G/A & 0                                   & 0                                   & 0                                   & 0                                   & 2                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 522                                 & 0                                   & 3                                   & Map\\_K10\\_VBC\\_CLI:23889\\_T/C   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 3                                  \\\\\n",
       "\t 522                                 & 0                                   & 3                                   & Map\\_K10\\_VBC\\_CLI:118442\\_T/A  & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 3                                  \\\\\n",
       "\t 522                                 & 0                                   & 3                                   & Map\\_K10\\_VBC\\_CLI:126882\\_A/C  & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 3                                  \\\\\n",
       "\t 522                                 & 0                                   & 3                                   & Map\\_K10\\_VBC\\_CLI:2160363\\_C/T & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 3                                  \\\\\n",
       "\t 522                                 & 0                                   & 3                                   & Map\\_K10\\_VBC\\_CLI:4040283\\_G/A & 0                                   & 0                                   & 0                                   & 0                                   & 3                                   & 0                                   & 0                                   & 0                                  \\\\\n",
       "\t 522                                 & 0                                   & 3                                   & Map\\_K10\\_VBC\\_CLI:4070036\\_C/A & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 3                                  \\\\\n",
       "\t 522                                 & 0                                   & 3                                   & Map\\_K10\\_VBC\\_CLI:4109267\\_A/C & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 0                                   & 3                                  \\\\\n",
       "\t ... & ... & ... & ... & ... & ... & ... & ... & ... & ... & ... & ...\\\\\n",
       "\t 502                                 &  4                                  &  19                                 & Map\\_K10\\_VBC\\_CLI:87442\\_A/G   & 1                                   &  3                                  & 0                                   & 0                                   &  7                                  &   7                                 &  4                                  &   1                                \\\\\n",
       "\t 502                                 &  4                                  &  19                                 & Map\\_K10\\_VBC\\_CLI:163876\\_A/G  & 1                                   &  3                                  & 0                                   & 0                                   &  7                                  &   7                                 &  4                                  &   1                                \\\\\n",
       "\t 502                                 &  4                                  &  19                                 & Map\\_K10\\_VBC\\_CLI:2083177\\_T/C & 1                                   &  3                                  & 0                                   & 0                                   &  7                                  &   7                                 &  4                                  &   1                                \\\\\n",
       "\t 477                                 &  4                                  &  44                                 & Map\\_K10\\_VBC\\_CLI:56276\\_T/C   & 4                                   &  0                                  & 0                                   & 0                                   & 33                                  &   5                                 &  2                                  &   4                                \\\\\n",
       "\t 518                                 &  5                                  &   2                                 & Map\\_K10\\_VBC\\_CLI:101109\\_G/T  & 0                                   &  5                                  & 0                                   & 0                                   &  0                                  &   2                                 &  0                                  &   0                                \\\\\n",
       "\t 514                                 &  5                                  &   6                                 & Map\\_K10\\_VBC\\_CLI:2026944\\_C/T & 2                                   &  3                                  & 0                                   & 0                                   &  3                                  &   2                                 &  1                                  &   0                                \\\\\n",
       "\t 514                                 &  5                                  &   6                                 & Map\\_K10\\_VBC\\_CLI:4053595\\_G/A & 2                                   &  3                                  & 0                                   & 0                                   &  3                                  &   2                                 &  1                                  &   0                                \\\\\n",
       "\t 509                                 &  5                                  &  11                                 & Map\\_K10\\_VBC\\_CLI:111061\\_G/A  & 5                                   &  0                                  & 0                                   & 0                                   & 11                                  &   0                                 &  0                                  &   0                                \\\\\n",
       "\t 505                                 &  5                                  &  15                                 & Map\\_K10\\_VBC\\_CLI:2174217\\_A/C & 5                                   &  0                                  & 0                                   & 0                                   & 14                                  &   0                                 &  0                                  &   1                                \\\\\n",
       "\t 505                                 &  5                                  &  15                                 & Map\\_K10\\_VBC\\_CLI:2174231\\_T/C & 5                                   &  0                                  & 0                                   & 0                                   & 14                                  &   0                                 &  0                                  &   1                                \\\\\n",
       "\t 502                                 &  5                                  &  18                                 & Map\\_K10\\_VBC\\_CLI:142835\\_G/C  & 1                                   &  4                                  & 0                                   & 0                                   &  7                                  &   6                                 &  4                                  &   1                                \\\\\n",
       "\t 502                                 &  5                                  &  18                                 & Map\\_K10\\_VBC\\_CLI:150857\\_G/C  & 1                                   &  4                                  & 0                                   & 0                                   &  7                                  &   6                                 &  4                                  &   1                                \\\\\n",
       "\t 502                                 &  5                                  &  18                                 & Map\\_K10\\_VBC\\_CLI:2172538\\_C/G & 1                                   &  4                                  & 0                                   & 0                                   &  7                                  &   6                                 &  4                                  &   1                                \\\\\n",
       "\t 501                                 &  5                                  &  19                                 & Map\\_K10\\_VBC\\_CLI:2059651\\_T/C & 1                                   &  4                                  & 0                                   & 0                                   &  7                                  &   7                                 &  4                                  &   1                                \\\\\n",
       "\t 195                                 &  5                                  & 325                                 & Map\\_K10\\_VBC\\_CLI:30901\\_A/C   & 0                                   &  5                                  & 0                                   & 0                                   &  0                                  & 145                                 &  4                                  & 176                                \\\\\n",
       "\t 195                                 &  5                                  & 325                                 & Map\\_K10\\_VBC\\_CLI:2189617\\_A/C & 0                                   &  5                                  & 0                                   & 0                                   &  0                                  & 145                                 &  4                                  & 176                                \\\\\n",
       "\t 195                                 &  5                                  & 325                                 & Map\\_K10\\_VBC\\_CLI:4040114\\_G/A & 0                                   &  5                                  & 0                                   & 0                                   &  0                                  & 145                                 &  4                                  & 176                                \\\\\n",
       "\t 194                                 &  5                                  & 326                                 & Map\\_K10\\_VBC\\_CLI:173146\\_C/T  & 0                                   &  5                                  & 0                                   & 0                                   &  0                                  & 146                                 &  4                                  & 176                                \\\\\n",
       "\t 501                                 &  6                                  &  18                                 & Map\\_K10\\_VBC\\_CLI:2054875\\_T/C & 1                                   &  5                                  & 0                                   & 0                                   &  7                                  &   6                                 &  4                                  &   1                                \\\\\n",
       "\t 465                                 &  6                                  &  54                                 & Map\\_K10\\_VBC\\_CLI:77507\\_C/A   & 5                                   &  1                                  & 0                                   & 0                                   & 14                                  &  13                                 & 21                                  &   6                                \\\\\n",
       "\t 465                                 &  6                                  &  54                                 & Map\\_K10\\_VBC\\_CLI:165969\\_C/T  & 5                                   &  1                                  & 0                                   & 0                                   & 14                                  &  13                                 & 21                                  &   6                                \\\\\n",
       "\t 465                                 &  6                                  &  54                                 & Map\\_K10\\_VBC\\_CLI:2151370\\_C/G & 5                                   &  1                                  & 0                                   & 0                                   & 14                                  &  13                                 & 21                                  &   6                                \\\\\n",
       "\t 465                                 &  6                                  &  54                                 & Map\\_K10\\_VBC\\_CLI:2167917\\_C/T & 5                                   &  1                                  & 0                                   & 0                                   & 14                                  &  13                                 & 21                                  &   6                                \\\\\n",
       "\t 193                                 &  6                                  & 326                                 & Map\\_K10\\_VBC\\_CLI:76286\\_G/T   & 0                                   &  6                                  & 0                                   & 0                                   &  0                                  & 146                                 &  4                                  & 176                                \\\\\n",
       "\t 516                                 &  7                                  &   2                                 & Map\\_K10\\_VBC\\_CLI:38870\\_A/G   & 0                                   &  7                                  & 0                                   & 0                                   &  0                                  &   2                                 &  0                                  &   0                                \\\\\n",
       "\t 515                                 &  7                                  &   3                                 & Map\\_K10\\_VBC\\_CLI:138160\\_G/A  & 0                                   &  7                                  & 0                                   & 0                                   &  0                                  &   3                                 &  0                                  &   0                                \\\\\n",
       "\t 514                                 &  8                                  &   3                                 & Map\\_K10\\_VBC\\_CLI:5726\\_C/T    & 0                                   &  8                                  & 0                                   & 0                                   &  0                                  &   3                                 &  0                                  &   0                                \\\\\n",
       "\t 441                                 & 12                                  &  72                                 & Map\\_K10\\_VBC\\_CLI:2168916\\_C/T & 0                                   & 12                                  & 0                                   & 0                                   &  0                                  &  67                                 &  3                                  &   2                                \\\\\n",
       "\t 478                                 & 14                                  &  33                                 & Map\\_K10\\_VBC\\_CLI:2126897\\_A/C & 0                                   & 14                                  & 0                                   & 0                                   &  0                                  &  33                                 &  0                                  &   0                                \\\\\n",
       "\t 458                                 & 15                                  &  52                                 & Map\\_K10\\_VBC\\_CLI:182378\\_G/A  & 0                                   & 15                                  & 0                                   & 0                                   &  0                                  &  52                                 &  0                                  &   0                                \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| AA | AB | BB | snp_id | MN_AB | NY_AB | PA_AB | VT_AB | MN_BB | NY_BB | PA_BB | VT_BB |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:6008_C/T    | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:9890_C/T    | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:10583_G/A   | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:28335_G/A   | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:49215_A/G   | 0                           | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:71631_G/A   | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:77046_G/T   | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:120560_C/T  | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:122449_C/T  | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:157436_G/T  | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:164089_C/T  | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:175227_A/G  | 0                           | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:2009251_G/A | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:2040397_G/C | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 2                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:2046193_C/T | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:4015985_G/A | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:4028613_G/A | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:4038386_G/A | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:4044695_G/A | 0                           | 0                           | 0                           | 0                           | 0                           | 1                           | 1                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:4072026_C/T | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:4088155_G/A | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:4111125_G/A | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           |\n",
       "| 523                         | 0                           | 2                           | Map_K10_VBC_CLI:4113491_G/A | 0                           | 0                           | 0                           | 0                           | 2                           | 0                           | 0                           | 0                           |\n",
       "| 522                         | 0                           | 3                           | Map_K10_VBC_CLI:23889_T/C   | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 3                           |\n",
       "| 522                         | 0                           | 3                           | Map_K10_VBC_CLI:118442_T/A  | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 3                           |\n",
       "| 522                         | 0                           | 3                           | Map_K10_VBC_CLI:126882_A/C  | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 3                           |\n",
       "| 522                         | 0                           | 3                           | Map_K10_VBC_CLI:2160363_C/T | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 3                           |\n",
       "| 522                         | 0                           | 3                           | Map_K10_VBC_CLI:4040283_G/A | 0                           | 0                           | 0                           | 0                           | 3                           | 0                           | 0                           | 0                           |\n",
       "| 522                         | 0                           | 3                           | Map_K10_VBC_CLI:4070036_C/A | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 3                           |\n",
       "| 522                         | 0                           | 3                           | Map_K10_VBC_CLI:4109267_A/C | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 0                           | 3                           |\n",
       "| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |\n",
       "| 502                         |  4                          |  19                         | Map_K10_VBC_CLI:87442_A/G   | 1                           |  3                          | 0                           | 0                           |  7                          |   7                         |  4                          |   1                         |\n",
       "| 502                         |  4                          |  19                         | Map_K10_VBC_CLI:163876_A/G  | 1                           |  3                          | 0                           | 0                           |  7                          |   7                         |  4                          |   1                         |\n",
       "| 502                         |  4                          |  19                         | Map_K10_VBC_CLI:2083177_T/C | 1                           |  3                          | 0                           | 0                           |  7                          |   7                         |  4                          |   1                         |\n",
       "| 477                         |  4                          |  44                         | Map_K10_VBC_CLI:56276_T/C   | 4                           |  0                          | 0                           | 0                           | 33                          |   5                         |  2                          |   4                         |\n",
       "| 518                         |  5                          |   2                         | Map_K10_VBC_CLI:101109_G/T  | 0                           |  5                          | 0                           | 0                           |  0                          |   2                         |  0                          |   0                         |\n",
       "| 514                         |  5                          |   6                         | Map_K10_VBC_CLI:2026944_C/T | 2                           |  3                          | 0                           | 0                           |  3                          |   2                         |  1                          |   0                         |\n",
       "| 514                         |  5                          |   6                         | Map_K10_VBC_CLI:4053595_G/A | 2                           |  3                          | 0                           | 0                           |  3                          |   2                         |  1                          |   0                         |\n",
       "| 509                         |  5                          |  11                         | Map_K10_VBC_CLI:111061_G/A  | 5                           |  0                          | 0                           | 0                           | 11                          |   0                         |  0                          |   0                         |\n",
       "| 505                         |  5                          |  15                         | Map_K10_VBC_CLI:2174217_A/C | 5                           |  0                          | 0                           | 0                           | 14                          |   0                         |  0                          |   1                         |\n",
       "| 505                         |  5                          |  15                         | Map_K10_VBC_CLI:2174231_T/C | 5                           |  0                          | 0                           | 0                           | 14                          |   0                         |  0                          |   1                         |\n",
       "| 502                         |  5                          |  18                         | Map_K10_VBC_CLI:142835_G/C  | 1                           |  4                          | 0                           | 0                           |  7                          |   6                         |  4                          |   1                         |\n",
       "| 502                         |  5                          |  18                         | Map_K10_VBC_CLI:150857_G/C  | 1                           |  4                          | 0                           | 0                           |  7                          |   6                         |  4                          |   1                         |\n",
       "| 502                         |  5                          |  18                         | Map_K10_VBC_CLI:2172538_C/G | 1                           |  4                          | 0                           | 0                           |  7                          |   6                         |  4                          |   1                         |\n",
       "| 501                         |  5                          |  19                         | Map_K10_VBC_CLI:2059651_T/C | 1                           |  4                          | 0                           | 0                           |  7                          |   7                         |  4                          |   1                         |\n",
       "| 195                         |  5                          | 325                         | Map_K10_VBC_CLI:30901_A/C   | 0                           |  5                          | 0                           | 0                           |  0                          | 145                         |  4                          | 176                         |\n",
       "| 195                         |  5                          | 325                         | Map_K10_VBC_CLI:2189617_A/C | 0                           |  5                          | 0                           | 0                           |  0                          | 145                         |  4                          | 176                         |\n",
       "| 195                         |  5                          | 325                         | Map_K10_VBC_CLI:4040114_G/A | 0                           |  5                          | 0                           | 0                           |  0                          | 145                         |  4                          | 176                         |\n",
       "| 194                         |  5                          | 326                         | Map_K10_VBC_CLI:173146_C/T  | 0                           |  5                          | 0                           | 0                           |  0                          | 146                         |  4                          | 176                         |\n",
       "| 501                         |  6                          |  18                         | Map_K10_VBC_CLI:2054875_T/C | 1                           |  5                          | 0                           | 0                           |  7                          |   6                         |  4                          |   1                         |\n",
       "| 465                         |  6                          |  54                         | Map_K10_VBC_CLI:77507_C/A   | 5                           |  1                          | 0                           | 0                           | 14                          |  13                         | 21                          |   6                         |\n",
       "| 465                         |  6                          |  54                         | Map_K10_VBC_CLI:165969_C/T  | 5                           |  1                          | 0                           | 0                           | 14                          |  13                         | 21                          |   6                         |\n",
       "| 465                         |  6                          |  54                         | Map_K10_VBC_CLI:2151370_C/G | 5                           |  1                          | 0                           | 0                           | 14                          |  13                         | 21                          |   6                         |\n",
       "| 465                         |  6                          |  54                         | Map_K10_VBC_CLI:2167917_C/T | 5                           |  1                          | 0                           | 0                           | 14                          |  13                         | 21                          |   6                         |\n",
       "| 193                         |  6                          | 326                         | Map_K10_VBC_CLI:76286_G/T   | 0                           |  6                          | 0                           | 0                           |  0                          | 146                         |  4                          | 176                         |\n",
       "| 516                         |  7                          |   2                         | Map_K10_VBC_CLI:38870_A/G   | 0                           |  7                          | 0                           | 0                           |  0                          |   2                         |  0                          |   0                         |\n",
       "| 515                         |  7                          |   3                         | Map_K10_VBC_CLI:138160_G/A  | 0                           |  7                          | 0                           | 0                           |  0                          |   3                         |  0                          |   0                         |\n",
       "| 514                         |  8                          |   3                         | Map_K10_VBC_CLI:5726_C/T    | 0                           |  8                          | 0                           | 0                           |  0                          |   3                         |  0                          |   0                         |\n",
       "| 441                         | 12                          |  72                         | Map_K10_VBC_CLI:2168916_C/T | 0                           | 12                          | 0                           | 0                           |  0                          |  67                         |  3                          |   2                         |\n",
       "| 478                         | 14                          |  33                         | Map_K10_VBC_CLI:2126897_A/C | 0                           | 14                          | 0                           | 0                           |  0                          |  33                         |  0                          |   0                         |\n",
       "| 458                         | 15                          |  52                         | Map_K10_VBC_CLI:182378_G/A  | 0                           | 15                          | 0                           | 0                           |  0                          |  52                         |  0                          |   0                         |\n",
       "\n"
      ],
      "text/plain": [
       "    AA  AB  BB  snp_id                      MN_AB NY_AB PA_AB VT_AB MN_BB NY_BB\n",
       "1   523 0   2   Map_K10_VBC_CLI:6008_C/T    0     0     0     0     2     0    \n",
       "2   523 0   2   Map_K10_VBC_CLI:9890_C/T    0     0     0     0     2     0    \n",
       "3   523 0   2   Map_K10_VBC_CLI:10583_G/A   0     0     0     0     0     0    \n",
       "4   523 0   2   Map_K10_VBC_CLI:28335_G/A   0     0     0     0     2     0    \n",
       "5   523 0   2   Map_K10_VBC_CLI:49215_A/G   0     0     0     0     0     2    \n",
       "6   523 0   2   Map_K10_VBC_CLI:71631_G/A   0     0     0     0     2     0    \n",
       "7   523 0   2   Map_K10_VBC_CLI:77046_G/T   0     0     0     0     2     0    \n",
       "8   523 0   2   Map_K10_VBC_CLI:120560_C/T  0     0     0     0     2     0    \n",
       "9   523 0   2   Map_K10_VBC_CLI:122449_C/T  0     0     0     0     0     0    \n",
       "10  523 0   2   Map_K10_VBC_CLI:157436_G/T  0     0     0     0     2     0    \n",
       "11  523 0   2   Map_K10_VBC_CLI:164089_C/T  0     0     0     0     2     0    \n",
       "12  523 0   2   Map_K10_VBC_CLI:175227_A/G  0     0     0     0     0     2    \n",
       "13  523 0   2   Map_K10_VBC_CLI:2009251_G/A 0     0     0     0     2     0    \n",
       "14  523 0   2   Map_K10_VBC_CLI:2040397_G/C 0     0     0     0     0     0    \n",
       "15  523 0   2   Map_K10_VBC_CLI:2046193_C/T 0     0     0     0     0     0    \n",
       "16  523 0   2   Map_K10_VBC_CLI:4015985_G/A 0     0     0     0     0     0    \n",
       "17  523 0   2   Map_K10_VBC_CLI:4028613_G/A 0     0     0     0     0     0    \n",
       "18  523 0   2   Map_K10_VBC_CLI:4038386_G/A 0     0     0     0     2     0    \n",
       "19  523 0   2   Map_K10_VBC_CLI:4044695_G/A 0     0     0     0     0     1    \n",
       "20  523 0   2   Map_K10_VBC_CLI:4072026_C/T 0     0     0     0     2     0    \n",
       "21  523 0   2   Map_K10_VBC_CLI:4088155_G/A 0     0     0     0     0     0    \n",
       "22  523 0   2   Map_K10_VBC_CLI:4111125_G/A 0     0     0     0     0     0    \n",
       "23  523 0   2   Map_K10_VBC_CLI:4113491_G/A 0     0     0     0     2     0    \n",
       "24  522 0   3   Map_K10_VBC_CLI:23889_T/C   0     0     0     0     0     0    \n",
       "25  522 0   3   Map_K10_VBC_CLI:118442_T/A  0     0     0     0     0     0    \n",
       "26  522 0   3   Map_K10_VBC_CLI:126882_A/C  0     0     0     0     0     0    \n",
       "27  522 0   3   Map_K10_VBC_CLI:2160363_C/T 0     0     0     0     0     0    \n",
       "28  522 0   3   Map_K10_VBC_CLI:4040283_G/A 0     0     0     0     3     0    \n",
       "29  522 0   3   Map_K10_VBC_CLI:4070036_C/A 0     0     0     0     0     0    \n",
       "30  522 0   3   Map_K10_VBC_CLI:4109267_A/C 0     0     0     0     0     0    \n",
       "... ... ... ... ...                         ...   ...   ...   ...   ...   ...  \n",
       "128 502  4   19 Map_K10_VBC_CLI:87442_A/G   1      3    0     0      7      7  \n",
       "129 502  4   19 Map_K10_VBC_CLI:163876_A/G  1      3    0     0      7      7  \n",
       "130 502  4   19 Map_K10_VBC_CLI:2083177_T/C 1      3    0     0      7      7  \n",
       "131 477  4   44 Map_K10_VBC_CLI:56276_T/C   4      0    0     0     33      5  \n",
       "132 518  5    2 Map_K10_VBC_CLI:101109_G/T  0      5    0     0      0      2  \n",
       "133 514  5    6 Map_K10_VBC_CLI:2026944_C/T 2      3    0     0      3      2  \n",
       "134 514  5    6 Map_K10_VBC_CLI:4053595_G/A 2      3    0     0      3      2  \n",
       "135 509  5   11 Map_K10_VBC_CLI:111061_G/A  5      0    0     0     11      0  \n",
       "136 505  5   15 Map_K10_VBC_CLI:2174217_A/C 5      0    0     0     14      0  \n",
       "137 505  5   15 Map_K10_VBC_CLI:2174231_T/C 5      0    0     0     14      0  \n",
       "138 502  5   18 Map_K10_VBC_CLI:142835_G/C  1      4    0     0      7      6  \n",
       "139 502  5   18 Map_K10_VBC_CLI:150857_G/C  1      4    0     0      7      6  \n",
       "140 502  5   18 Map_K10_VBC_CLI:2172538_C/G 1      4    0     0      7      6  \n",
       "141 501  5   19 Map_K10_VBC_CLI:2059651_T/C 1      4    0     0      7      7  \n",
       "142 195  5  325 Map_K10_VBC_CLI:30901_A/C   0      5    0     0      0    145  \n",
       "143 195  5  325 Map_K10_VBC_CLI:2189617_A/C 0      5    0     0      0    145  \n",
       "144 195  5  325 Map_K10_VBC_CLI:4040114_G/A 0      5    0     0      0    145  \n",
       "145 194  5  326 Map_K10_VBC_CLI:173146_C/T  0      5    0     0      0    146  \n",
       "146 501  6   18 Map_K10_VBC_CLI:2054875_T/C 1      5    0     0      7      6  \n",
       "147 465  6   54 Map_K10_VBC_CLI:77507_C/A   5      1    0     0     14     13  \n",
       "148 465  6   54 Map_K10_VBC_CLI:165969_C/T  5      1    0     0     14     13  \n",
       "149 465  6   54 Map_K10_VBC_CLI:2151370_C/G 5      1    0     0     14     13  \n",
       "150 465  6   54 Map_K10_VBC_CLI:2167917_C/T 5      1    0     0     14     13  \n",
       "151 193  6  326 Map_K10_VBC_CLI:76286_G/T   0      6    0     0      0    146  \n",
       "152 516  7    2 Map_K10_VBC_CLI:38870_A/G   0      7    0     0      0      2  \n",
       "153 515  7    3 Map_K10_VBC_CLI:138160_G/A  0      7    0     0      0      3  \n",
       "154 514  8    3 Map_K10_VBC_CLI:5726_C/T    0      8    0     0      0      3  \n",
       "155 441 12   72 Map_K10_VBC_CLI:2168916_C/T 0     12    0     0      0     67  \n",
       "156 478 14   33 Map_K10_VBC_CLI:2126897_A/C 0     14    0     0      0     33  \n",
       "157 458 15   52 Map_K10_VBC_CLI:182378_G/A  0     15    0     0      0     52  \n",
       "    PA_BB VT_BB\n",
       "1   0     0    \n",
       "2   0     0    \n",
       "3   2     0    \n",
       "4   0     0    \n",
       "5   0     0    \n",
       "6   0     0    \n",
       "7   0     0    \n",
       "8   0     0    \n",
       "9   2     0    \n",
       "10  0     0    \n",
       "11  0     0    \n",
       "12  0     0    \n",
       "13  0     0    \n",
       "14  0     2    \n",
       "15  2     0    \n",
       "16  2     0    \n",
       "17  2     0    \n",
       "18  0     0    \n",
       "19  1     0    \n",
       "20  0     0    \n",
       "21  2     0    \n",
       "22  2     0    \n",
       "23  0     0    \n",
       "24  0     3    \n",
       "25  0     3    \n",
       "26  0     3    \n",
       "27  0     3    \n",
       "28  0     0    \n",
       "29  0     3    \n",
       "30  0     3    \n",
       "... ...   ...  \n",
       "128  4      1  \n",
       "129  4      1  \n",
       "130  4      1  \n",
       "131  2      4  \n",
       "132  0      0  \n",
       "133  1      0  \n",
       "134  1      0  \n",
       "135  0      0  \n",
       "136  0      1  \n",
       "137  0      1  \n",
       "138  4      1  \n",
       "139  4      1  \n",
       "140  4      1  \n",
       "141  4      1  \n",
       "142  4    176  \n",
       "143  4    176  \n",
       "144  4    176  \n",
       "145  4    176  \n",
       "146  4      1  \n",
       "147 21      6  \n",
       "148 21      6  \n",
       "149 21      6  \n",
       "150 21      6  \n",
       "151  4    176  \n",
       "152  0      0  \n",
       "153  0      0  \n",
       "154  0      0  \n",
       "155  3      2  \n",
       "156  0      0  \n",
       "157  0      0  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "df %>% \n",
    "    arrange(AB)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 95,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "     \n",
       "      0/0 0/1 1/1\n",
       "  0/0 465   0   0\n",
       "  0/1   0   6   0\n",
       "  1/1   0   0  54"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "table(GT['Map_K10_VBC_CLI:77507_C/A', ], GT['Map_K10_VBC_CLI:165969_C/T', ])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 173,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>x</th><th scope=col>y</th><th scope=col>n_heterozygous</th><th scope=col>cow_id</th><th scope=col>type_1</th><th scope=col>type_2</th><th scope=col>farm</th><th scope=col>contamination</th><th scope=col>date</th><th scope=col>state</th><th scope=col>mix</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>MAP129</th><td> 3.668753               </td><td>-3.303833               </td><td>29                      </td><td>1283                    </td><td>tissue                  </td><td>Ileum_20cm_from_IC_Valve</td><td>9                       </td><td>0                       </td><td>2006                    </td><td>NY                      </td><td>1                       </td></tr>\n",
       "\t<tr><th scope=row>MAP022</th><td> 2.441327               </td><td>-1.987906               </td><td> 8                      </td><td>1085                    </td><td>fecal                   </td><td>fecal                   </td><td>9                       </td><td>0                       </td><td>2004                    </td><td>NY                      </td><td>0                       </td></tr>\n",
       "\t<tr><th scope=row>MAP153</th><td> 2.240757               </td><td> 3.020176               </td><td> 6                      </td><td>1181                    </td><td>tissue                  </td><td>LymphNode1              </td><td>9                       </td><td>0                       </td><td>2006                    </td><td>NY                      </td><td>1                       </td></tr>\n",
       "\t<tr><th scope=row>MAP160</th><td>-3.466697               </td><td>-3.564802               </td><td> 2                      </td><td>1355                    </td><td>tissue                  </td><td>Ileum_20cm_from_IC_Valve</td><td>9                       </td><td>0                       </td><td>2006                    </td><td>NY                      </td><td>0                       </td></tr>\n",
       "\t<tr><th scope=row>MAP168</th><td> 3.756924               </td><td> 8.876470               </td><td> 3                      </td><td>1645                    </td><td>fecal                   </td><td>fecal                   </td><td>9                       </td><td>0                       </td><td>2006                    </td><td>NY                      </td><td>0                       </td></tr>\n",
       "\t<tr><th scope=row>MAP140</th><td>-4.535493               </td><td>-4.579195               </td><td>12                      </td><td>2158                    </td><td>tissue                  </td><td>LymphNode2              </td><td>9                       </td><td>0                       </td><td>2006                    </td><td>NY                      </td><td>1                       </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|lllllllllll}\n",
       "  & x & y & n\\_heterozygous & cow\\_id & type\\_1 & type\\_2 & farm & contamination & date & state & mix\\\\\n",
       "\\hline\n",
       "\tMAP129 &  3.668753                        & -3.303833                        & 29                               & 1283                             & tissue                           & Ileum\\_20cm\\_from\\_IC\\_Valve & 9                                & 0                                & 2006                             & NY                               & 1                               \\\\\n",
       "\tMAP022 &  2.441327                & -1.987906                &  8                       & 1085                     & fecal                    & fecal                    & 9                        & 0                        & 2004                     & NY                       & 0                       \\\\\n",
       "\tMAP153 &  2.240757                &  3.020176                &  6                       & 1181                     & tissue                   & LymphNode1               & 9                        & 0                        & 2006                     & NY                       & 1                       \\\\\n",
       "\tMAP160 & -3.466697                        & -3.564802                        &  2                               & 1355                             & tissue                           & Ileum\\_20cm\\_from\\_IC\\_Valve & 9                                & 0                                & 2006                             & NY                               & 0                               \\\\\n",
       "\tMAP168 &  3.756924                &  8.876470                &  3                       & 1645                     & fecal                    & fecal                    & 9                        & 0                        & 2006                     & NY                       & 0                       \\\\\n",
       "\tMAP140 & -4.535493                & -4.579195                & 12                       & 2158                     & tissue                   & LymphNode2               & 9                        & 0                        & 2006                     & NY                       & 1                       \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | x | y | n_heterozygous | cow_id | type_1 | type_2 | farm | contamination | date | state | mix |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| MAP129 |  3.668753                | -3.303833                | 29                       | 1283                     | tissue                   | Ileum_20cm_from_IC_Valve | 9                        | 0                        | 2006                     | NY                       | 1                        |\n",
       "| MAP022 |  2.441327                | -1.987906                |  8                       | 1085                     | fecal                    | fecal                    | 9                        | 0                        | 2004                     | NY                       | 0                        |\n",
       "| MAP153 |  2.240757                |  3.020176                |  6                       | 1181                     | tissue                   | LymphNode1               | 9                        | 0                        | 2006                     | NY                       | 1                        |\n",
       "| MAP160 | -3.466697                | -3.564802                |  2                       | 1355                     | tissue                   | Ileum_20cm_from_IC_Valve | 9                        | 0                        | 2006                     | NY                       | 0                        |\n",
       "| MAP168 |  3.756924                |  8.876470                |  3                       | 1645                     | fecal                    | fecal                    | 9                        | 0                        | 2006                     | NY                       | 0                        |\n",
       "| MAP140 | -4.535493                | -4.579195                | 12                       | 2158                     | tissue                   | LymphNode2               | 9                        | 0                        | 2006                     | NY                       | 1                        |\n",
       "\n"
      ],
      "text/plain": [
       "       x         y         n_heterozygous cow_id type_1\n",
       "MAP129  3.668753 -3.303833 29             1283   tissue\n",
       "MAP022  2.441327 -1.987906  8             1085   fecal \n",
       "MAP153  2.240757  3.020176  6             1181   tissue\n",
       "MAP160 -3.466697 -3.564802  2             1355   tissue\n",
       "MAP168  3.756924  8.876470  3             1645   fecal \n",
       "MAP140 -4.535493 -4.579195 12             2158   tissue\n",
       "       type_2                   farm contamination date state mix\n",
       "MAP129 Ileum_20cm_from_IC_Valve 9    0             2006 NY    1  \n",
       "MAP022 fecal                    9    0             2004 NY    0  \n",
       "MAP153 LymphNode1               9    0             2006 NY    1  \n",
       "MAP160 Ileum_20cm_from_IC_Valve 9    0             2006 NY    0  \n",
       "MAP168 fecal                    9    0             2006 NY    0  \n",
       "MAP140 LymphNode2               9    0             2006 NY    1  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "d <- data.frame(\n",
    "    x = y_tsne[, 1], \n",
    "    y = y_tsne[, 2],\n",
    "    n_heterozygous = (X_no_orphan > 0.1 & X_no_orphan < 0.9) %>% colSums(),\n",
    "    cow_id = meta$CowID,\n",
    "    type_1 = meta$Type %>% factor(),\n",
    "    type_2 = meta$Type2 %>% factor(),\n",
    "    farm = meta$Farm %>% factor(),\n",
    "    contamination = meta$Contamination %>% factor(),\n",
    "    date = meta$Date %>% factor(),\n",
    "    state = meta$State %>% factor(),\n",
    "    mix = meta$Mix %>% factor()\n",
    ")\n",
    "head(d)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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