RunTILTools.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "suppressPackageStartupMessages({\n",
    "    # Tidyverse\n",
    "    library('dplyr')\n",
    "    library('readr')\n",
    "    library('purrr')\n",
    "    library('glue')\n",
    "    library('stringr')\n",
    "    library('tibble')\n",
    "\n",
    "    # Bioinformatics - Helpers\n",
    "    library('biomaRt')  # ID-mapping\n",
    "    library('tximport')  # For smooth kallisto imports\n",
    "\n",
    "    # Bioinformatics - Analyses tools\n",
    "    library('estimate')  # http://bioinformatics.mdanderson.org/estimate/\n",
    "    library('xCell')  # https://github.com/dviraran/xCell\n",
    "    library('MCPcounter')\n",
    "    # ... and we have CIBERSORT as a Java/R hybrid application\n",
    "})\n",
    "\n",
    "# Show traceback on runtime error!\n",
    "options(error=function() { traceback(2); q() })\n",
    "\n",
    "# Other helpers\n",
    "head3 <- function(x, ...) { head(x, n=3, ...) }\n",
    "\n",
    "## simple wrapper for running shell commands\n",
    "shell <- function(cmdargs, command=\"bash\") {\n",
    "    # We need the full path to the main program\n",
    "    command_path <- Sys.which(command)\n",
    "    system(glue(\"{command_path} {cmdargs}\"))\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "get_expression_data <- function(tmpdir) {\n",
    "    expression_name <- glue(\"{tmpdir}/gene-expression-matrix.csv\")\n",
    "    if (file.exists(expression_name)) {\n",
    "        return(read_csv(expression_name) %>%\n",
    "                    data.frame() %>%\n",
    "                    tibble::column_to_rownames(\"Gene_symbol\"))\n",
    "    }\n",
    "\n",
    "    mart <- useMart(biomart=\"ENSEMBL_MART_ENSEMBL\", dataset=\"hsapiens_gene_ensembl\", host=\"ensembl.org\")\n",
    "    t2g <- getBM(attributes=c(\"ensembl_transcript_id\", \"external_gene_name\"), mart=mart)\n",
    "    t2g <- dplyr::rename(t2g, target_id=ensembl_transcript_id, ext_gene=external_gene_name)\n",
    "    head(t2g)\n",
    "\n",
    "    kallisto_files <- dir('data', recursive=TRUE, full.names=TRUE, pattern=\"*.tsv\")\n",
    "\n",
    "    # Import and reduce\n",
    "    txi <- tximport(kallisto_files, type=\"kallisto\", tx2gene=t2g)\n",
    "    expression_data <- txi$counts\n",
    "\n",
    "    # RCC and Kallisto names are redundant and can be omitted\n",
    "    # Makes columns patient identifiers\n",
    "    colnames(expression_data) <- kallisto_files %>% \n",
    "                                    str_replace(\"-kallisto/abundance.tsv\", \"\") %>%\n",
    "                                    str_replace(\"data/\", \"\") %>%\n",
    "                                    str_replace_all(\"-|_\", \".\")\n",
    "    head3(expression_data)\n",
    "\n",
    "    expression_data %>%\n",
    "        as.data.frame %>%\n",
    "        tibble::rownames_to_column(\"Gene_symbol\") %>%\n",
    "        write_csv(path=expression_name)\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "run_cibersort <- function(expression_data, tmpdir) {\n",
    "    cibersort_home_dir <- glue(\"{tmpdir}/cibersort\")\n",
    "\n",
    "    lm22_path <- glue(\"{cibersort_home_dir}/LM22.txt\")\n",
    "    lm22_df <- read_tsv(lm22_path)\n",
    "    head3(lm22_df)\n",
    "\n",
    "    lm22_genes <- lm22_df %>% dplyr::select(`Gene symbol`) %>% flatten_chr\n",
    "    lm22_rel_genes <- intersect(rownames(expression_data), lm22_genes)\n",
    "    print(\n",
    "      paste(\n",
    "        length(lm22_rel_genes), \"out of\", length(lm22_genes),\n",
    "        \"LM22 genes are present in the expression data\"\n",
    "      )\n",
    "    )\n",
    "\n",
    "    # Filter the matrix down to LM22 genes\n",
    "    expression_data_lm22 <- expression_data[lm22_rel_genes, ]\n",
    "    head(expression_data_lm22)\n",
    "    dim(expression_data_lm22)\n",
    "\n",
    "    # Filter out genes where we have almost no data (i.e. top 10%), and write out as\n",
    "    # an input file for CIBERSORT.\n",
    "    cibersort_input <- glue(\"{tmpdir}/cibersort-input.tsv\")\n",
    "    low_expression_threshold <- 1\n",
    "    test <- expression_data_lm22 %>%\n",
    "        data.frame() %>%\n",
    "        tibble::rownames_to_column(\"Gene_symbols\") %>%\n",
    "        mutate(low_cnt=rowSums(.[-1] < low_expression_threshold)) %>%\n",
    "        filter(low_cnt < quantile(low_cnt, .90)) %>%  # FIXME: Changed from `<` to `<=`...didn't work when low_cnt was 0 for most/all.\n",
    "        dplyr::select(-low_cnt) %>%\n",
    "        write_tsv(cibersort_input) %>%\n",
    "        dim() # +1 column since we added the indices back to table for convenience\n",
    "\n",
    "    # Run CIIBERSORT\n",
    "    library(Rserve)\n",
    "    Rserve(args=\"--no-save\")\n",
    "    shell(\n",
    "        command=\"java\",\n",
    "        glue(\n",
    "         \"-Xmx10g -Xms3g \\\\\n",
    "          -jar {cibersort_home_dir}/CIBERSORT.jar \\\\\n",
    "          -M {cibersort_input} -B {lm22_path} \\\\\n",
    "          > {tmpdir}/cibersort-output.tsv\n",
    "          2> {tmpdir}/cibersort.err.log\"\n",
    "        )  # by default results are printed to stdout\n",
    "    )\n",
    "    shell(command=\"pkill\", \"-9 Rserve\")  # no need to be graceful here\n",
    "\n",
    "    # Read in results\n",
    "    cibersort <- read_delim(glue(\"{tmpdir}/cibersort-output.tsv\"), delim=\"\\t\", comment=\">\", trim_ws=TRUE)\n",
    "    head(cibersort)\n",
    "\n",
    "    # The CIBERSORT output has an extra tab at the end of the headers row, so it adds\n",
    "    # in this extra column `X27` with no data. The output also contains a column called\n",
    "    # `Column` that just numbers each row. Remove both of these here.\n",
    "    cibersort.df <- cibersort %>%\n",
    "                        data.frame %>%\n",
    "                        dplyr::select(-`X27`, -`Column`)\n",
    "    sampleNames <- colnames(expression_data_lm22)\n",
    "    row.names(cibersort.df) <- sampleNames\n",
    "    \n",
    "    cibersort.df %>%\n",
    "        tibble::rownames_to_column(\"Sample Name\") %>%\n",
    "        write_tsv(glue(\"{tmpdir}/cibersort-output.tsv\"))\n",
    "\n",
    "    cibersort.df\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "run_estimate <- function(expression_data, tmpdir) {\n",
    "    # Convert our expression matrix into GCT format and save it to be \n",
    "    # used by ESTIMATE\n",
    "    estimate_input <- glue(\"{tmpdir}/estimate-input.gct\")\n",
    "\n",
    "    outputGCT(expression_data, estimate_input)\n",
    "\n",
    "    # Run ESTIMATE and save the results into another GCT file\n",
    "    estimate_output <- glue('{tmpdir}/estimate-output.gct')\n",
    "    estimateScore(estimate_input, output.ds=estimate_output, platform=\"illumina\")\n",
    "\n",
    "    # Load them back and return\n",
    "    estimate_df <- read_tsv(estimate_output, comment=\"#\", skip=1) %>%\n",
    "                        dplyr::select(-`NAME`) %>%\n",
    "                        as.data.frame\n",
    "    estimate_df %>%\n",
    "        column_to_rownames(\"Description\")\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "run_xcell <- function(expression_data, tmpdir) {\n",
    "    xcell_res <- xCellAnalysis(expression_data,\n",
    "                               save.raw=TRUE,  # This produces a second output file with untransformed scores.\n",
    "                               file.name=glue('{tmpdir}/xcell-output'))\n",
    "    \n",
    "    xcell_output <- glue('{tmpdir}/xcell-output.tsv')\n",
    "    xcell_res %>%\n",
    "        as.data.frame %>%\n",
    "        rownames_to_column(\"CellType\") %>%\n",
    "        write_tsv(xcell_output)\n",
    "    xcell_res\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "run_mcpcounter <- function(expression_data, tmpdir) {\n",
    "    mcp_res <- MCPcounter.estimate(expression_data, featuresType=\"HUGO_symbols\")\n",
    "    mcp_output <- glue(\"{tmpdir}/mcpcounter-output.tsv\")\n",
    "    mcp_res %>%\n",
    "        as.data.frame %>%\n",
    "        rownames_to_column(\"CellType\") %>%\n",
    "        write_tsv(mcp_output)\n",
    "    mcp_res\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Parsed with column specification:\n",
      "cols(\n",
      "  .default = col_double(),\n",
      "  Gene_symbol = col_character()\n",
      ")\n",
      "See spec(...) for full column specifications.\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>gerald.H5NKVBBXX.4.CGGCTATG.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.4.CTGAAGCT.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.4.TAATGCGC.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.4.TAATGCGC.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.4.TCTCGCGC.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.5.ATTACTCG.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.5.ATTACTCG.CCTATCCT</th><th scope=col>gerald.H5NKVBBXX.5.ATTACTCG.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.5.ATTCAGAA.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.5.CGCTCATT.ATAGAGGC</th><th scope=col>⋯</th><th scope=col>gerald.H5NKVBBXX.6.TCCGCGAA.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.6.TCCGCGAA.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.6.TCTCGCGC.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.ATTCAGAA.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.CGCTCATT.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.CTGAAGCT.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.GAATTCGT.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.GAGATTCC.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.7.GAGATTCC.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.TCCGGAGA.CCTATCCT</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>A1BG</th><td>  160.2753 </td><td>  29.19838 </td><td>  89.983320</td><td> 172.5639  </td><td>  118.00680</td><td>  365.7986 </td><td>  231.9847 </td><td>  458.5096 </td><td>  425.8787 </td><td> 1176.1113 </td><td>⋯          </td><td>  578.7028 </td><td>2938.4187  </td><td> 133.3406  </td><td>  449.5915 </td><td>1032.19420 </td><td> 1121.0535 </td><td> 1016.4681 </td><td>  931.8012 </td><td>  966.2057 </td><td>  300.1420 </td></tr>\n",
       "\t<tr><th scope=row>A1CF</th><td>  103.0000 </td><td>   9.00387 </td><td>   6.999996</td><td> 208.0000  </td><td>   76.01059</td><td>  288.0374 </td><td>   16.0156 </td><td>  261.2861 </td><td>  144.5596 </td><td>  134.9335 </td><td>⋯          </td><td>  166.0010 </td><td> 183.0124  </td><td> 106.0640  </td><td>  125.0098 </td><td>  15.00308 </td><td>  130.5271 </td><td>  298.9732 </td><td>  222.0008 </td><td>  273.0109 </td><td>  450.0056 </td></tr>\n",
       "\t<tr><th scope=row>A2M</th><td>53163.7239 </td><td>6305.79310 </td><td>6032.217320</td><td>2788.6935  </td><td>12548.85321</td><td>14220.8857 </td><td>52604.2210 </td><td>39731.8083 </td><td>53494.5108 </td><td>20731.3946 </td><td>⋯          </td><td>55476.2603 </td><td>6677.8170  </td><td>7270.9104  </td><td>85258.1091 </td><td>5215.15598 </td><td>20041.5642 </td><td>26814.7081 </td><td>25570.4671 </td><td>93369.1144 </td><td>50277.6901 </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllllllllllllllllllllllll}\n",
       "  & gerald.H5NKVBBXX.4.CGGCTATG.TATAGCCT & gerald.H5NKVBBXX.4.CTGAAGCT.ATAGAGGC & gerald.H5NKVBBXX.4.TAATGCGC.ATAGAGGC & gerald.H5NKVBBXX.4.TAATGCGC.TATAGCCT & gerald.H5NKVBBXX.4.TCTCGCGC.ATAGAGGC & gerald.H5NKVBBXX.5.ATTACTCG.ATAGAGGC & gerald.H5NKVBBXX.5.ATTACTCG.CCTATCCT & gerald.H5NKVBBXX.5.ATTACTCG.TATAGCCT & gerald.H5NKVBBXX.5.ATTCAGAA.ATAGAGGC & gerald.H5NKVBBXX.5.CGCTCATT.ATAGAGGC & ⋯ & gerald.H5NKVBBXX.6.TCCGCGAA.ATAGAGGC & gerald.H5NKVBBXX.6.TCCGCGAA.TATAGCCT & gerald.H5NKVBBXX.6.TCTCGCGC.TATAGCCT & gerald.H5NKVBBXX.7.ATTCAGAA.TATAGCCT & gerald.H5NKVBBXX.7.CGCTCATT.TATAGCCT & gerald.H5NKVBBXX.7.CTGAAGCT.TATAGCCT & gerald.H5NKVBBXX.7.GAATTCGT.TATAGCCT & gerald.H5NKVBBXX.7.GAGATTCC.ATAGAGGC & gerald.H5NKVBBXX.7.GAGATTCC.TATAGCCT & gerald.H5NKVBBXX.7.TCCGGAGA.CCTATCCT\\\\\n",
       "\\hline\n",
       "\tA1BG &   160.2753  &   29.19838  &   89.983320 &  172.5639   &   118.00680 &   365.7986  &   231.9847  &   458.5096  &   425.8787  &  1176.1113  & ⋯           &   578.7028  & 2938.4187   &  133.3406   &   449.5915  & 1032.19420  &  1121.0535  &  1016.4681  &   931.8012  &   966.2057  &   300.1420 \\\\\n",
       "\tA1CF &   103.0000  &    9.00387  &    6.999996 &  208.0000   &    76.01059 &   288.0374  &    16.0156  &   261.2861  &   144.5596  &   134.9335  & ⋯           &   166.0010  &  183.0124   &  106.0640   &   125.0098  &   15.00308  &   130.5271  &   298.9732  &   222.0008  &   273.0109  &   450.0056 \\\\\n",
       "\tA2M & 53163.7239  & 6305.79310  & 6032.217320 & 2788.6935   & 12548.85321 & 14220.8857  & 52604.2210  & 39731.8083  & 53494.5108  & 20731.3946  & ⋯           & 55476.2603  & 6677.8170   & 7270.9104   & 85258.1091  & 5215.15598  & 20041.5642  & 26814.7081  & 25570.4671  & 93369.1144  & 50277.6901 \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | gerald.H5NKVBBXX.4.CGGCTATG.TATAGCCT | gerald.H5NKVBBXX.4.CTGAAGCT.ATAGAGGC | gerald.H5NKVBBXX.4.TAATGCGC.ATAGAGGC | gerald.H5NKVBBXX.4.TAATGCGC.TATAGCCT | gerald.H5NKVBBXX.4.TCTCGCGC.ATAGAGGC | gerald.H5NKVBBXX.5.ATTACTCG.ATAGAGGC | gerald.H5NKVBBXX.5.ATTACTCG.CCTATCCT | gerald.H5NKVBBXX.5.ATTACTCG.TATAGCCT | gerald.H5NKVBBXX.5.ATTCAGAA.ATAGAGGC | gerald.H5NKVBBXX.5.CGCTCATT.ATAGAGGC | ⋯ | gerald.H5NKVBBXX.6.TCCGCGAA.ATAGAGGC | gerald.H5NKVBBXX.6.TCCGCGAA.TATAGCCT | gerald.H5NKVBBXX.6.TCTCGCGC.TATAGCCT | gerald.H5NKVBBXX.7.ATTCAGAA.TATAGCCT | gerald.H5NKVBBXX.7.CGCTCATT.TATAGCCT | gerald.H5NKVBBXX.7.CTGAAGCT.TATAGCCT | gerald.H5NKVBBXX.7.GAATTCGT.TATAGCCT | gerald.H5NKVBBXX.7.GAGATTCC.ATAGAGGC | gerald.H5NKVBBXX.7.GAGATTCC.TATAGCCT | gerald.H5NKVBBXX.7.TCCGGAGA.CCTATCCT | \n",
       "|---|---|---|\n",
       "| A1BG |   160.2753  |   29.19838  |   89.983320 |  172.5639   |   118.00680 |   365.7986  |   231.9847  |   458.5096  |   425.8787  |  1176.1113  | ⋯           |   578.7028  | 2938.4187   |  133.3406   |   449.5915  | 1032.19420  |  1121.0535  |  1016.4681  |   931.8012  |   966.2057  |   300.1420  | \n",
       "| A1CF |   103.0000  |    9.00387  |    6.999996 |  208.0000   |    76.01059 |   288.0374  |    16.0156  |   261.2861  |   144.5596  |   134.9335  | ⋯           |   166.0010  |  183.0124   |  106.0640   |   125.0098  |   15.00308  |   130.5271  |   298.9732  |   222.0008  |   273.0109  |   450.0056  | \n",
       "| A2M | 53163.7239  | 6305.79310  | 6032.217320 | 2788.6935   | 12548.85321 | 14220.8857  | 52604.2210  | 39731.8083  | 53494.5108  | 20731.3946  | ⋯           | 55476.2603  | 6677.8170   | 7270.9104   | 85258.1091  | 5215.15598  | 20041.5642  | 26814.7081  | 25570.4671  | 93369.1144  | 50277.6901  | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "     gerald.H5NKVBBXX.4.CGGCTATG.TATAGCCT gerald.H5NKVBBXX.4.CTGAAGCT.ATAGAGGC\n",
       "A1BG   160.2753                             29.19838                          \n",
       "A1CF   103.0000                              9.00387                          \n",
       "A2M  53163.7239                           6305.79310                          \n",
       "     gerald.H5NKVBBXX.4.TAATGCGC.ATAGAGGC gerald.H5NKVBBXX.4.TAATGCGC.TATAGCCT\n",
       "A1BG   89.983320                           172.5639                           \n",
       "A1CF    6.999996                           208.0000                           \n",
       "A2M  6032.217320                          2788.6935                           \n",
       "     gerald.H5NKVBBXX.4.TCTCGCGC.ATAGAGGC gerald.H5NKVBBXX.5.ATTACTCG.ATAGAGGC\n",
       "A1BG   118.00680                            365.7986                          \n",
       "A1CF    76.01059                            288.0374                          \n",
       "A2M  12548.85321                          14220.8857                          \n",
       "     gerald.H5NKVBBXX.5.ATTACTCG.CCTATCCT gerald.H5NKVBBXX.5.ATTACTCG.TATAGCCT\n",
       "A1BG   231.9847                             458.5096                          \n",
       "A1CF    16.0156                             261.2861                          \n",
       "A2M  52604.2210                           39731.8083                          \n",
       "     gerald.H5NKVBBXX.5.ATTCAGAA.ATAGAGGC gerald.H5NKVBBXX.5.CGCTCATT.ATAGAGGC\n",
       "A1BG   425.8787                            1176.1113                          \n",
       "A1CF   144.5596                             134.9335                          \n",
       "A2M  53494.5108                           20731.3946                          \n",
       "     ⋯ gerald.H5NKVBBXX.6.TCCGCGAA.ATAGAGGC\n",
       "A1BG ⋯   578.7028                          \n",
       "A1CF ⋯   166.0010                          \n",
       "A2M  ⋯ 55476.2603                          \n",
       "     gerald.H5NKVBBXX.6.TCCGCGAA.TATAGCCT gerald.H5NKVBBXX.6.TCTCGCGC.TATAGCCT\n",
       "A1BG 2938.4187                             133.3406                           \n",
       "A1CF  183.0124                             106.0640                           \n",
       "A2M  6677.8170                            7270.9104                           \n",
       "     gerald.H5NKVBBXX.7.ATTCAGAA.TATAGCCT gerald.H5NKVBBXX.7.CGCTCATT.TATAGCCT\n",
       "A1BG   449.5915                           1032.19420                          \n",
       "A1CF   125.0098                             15.00308                          \n",
       "A2M  85258.1091                           5215.15598                          \n",
       "     gerald.H5NKVBBXX.7.CTGAAGCT.TATAGCCT gerald.H5NKVBBXX.7.GAATTCGT.TATAGCCT\n",
       "A1BG  1121.0535                            1016.4681                          \n",
       "A1CF   130.5271                             298.9732                          \n",
       "A2M  20041.5642                           26814.7081                          \n",
       "     gerald.H5NKVBBXX.7.GAGATTCC.ATAGAGGC gerald.H5NKVBBXX.7.GAGATTCC.TATAGCCT\n",
       "A1BG   931.8012                             966.2057                          \n",
       "A1CF   222.0008                             273.0109                          \n",
       "A2M  25570.4671                           93369.1144                          \n",
       "     gerald.H5NKVBBXX.7.TCCGGAGA.CCTATCCT\n",
       "A1BG   300.1420                          \n",
       "A1CF   450.0056                          \n",
       "A2M  50277.6901                          "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>gerald.H5NKVBBXX.4.CGGCTATG.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.4.CTGAAGCT.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.4.TAATGCGC.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.4.TAATGCGC.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.4.TCTCGCGC.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.5.ATTACTCG.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.5.ATTACTCG.CCTATCCT</th><th scope=col>gerald.H5NKVBBXX.5.ATTACTCG.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.5.ATTCAGAA.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.5.CGCTCATT.ATAGAGGC</th><th scope=col>⋯</th><th scope=col>gerald.H5NKVBBXX.6.TCCGCGAA.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.6.TCCGCGAA.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.6.TCTCGCGC.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.ATTCAGAA.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.CGCTCATT.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.CTGAAGCT.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.GAATTCGT.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.GAGATTCC.ATAGAGGC</th><th scope=col>gerald.H5NKVBBXX.7.GAGATTCC.TATAGCCT</th><th scope=col>gerald.H5NKVBBXX.7.TCCGGAGA.CCTATCCT</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>T cells</th><td>  258.03017 </td><td>  42.369740 </td><td>   63.672543</td><td> 158.37900  </td><td> 565.26341  </td><td>  383.62473 </td><td>   127.12544</td><td>   512.77558</td><td>  343.97235 </td><td> 1190.88239 </td><td>⋯           </td><td>  241.35106 </td><td>  290.10382 </td><td> 252.31332  </td><td>  240.35471 </td><td>  293.85645 </td><td>  369.86630 </td><td>  868.87871 </td><td>  503.36622 </td><td>   423.55900</td><td>  968.3559  </td></tr>\n",
       "\t<tr><th scope=row>CD8 T cells</th><td>  128.41972 </td><td>   4.993360 </td><td>   20.999990</td><td> 229.00000  </td><td> 152.95100  </td><td>   25.99999 </td><td>     0.00000</td><td>   329.00000</td><td>  160.25034 </td><td>  232.92266 </td><td>⋯           </td><td>  163.30978 </td><td>  120.42475 </td><td> 178.99980  </td><td>  104.09030 </td><td>  340.22100 </td><td>   76.96831 </td><td>  395.32420 </td><td>  155.34520 </td><td>   154.45260</td><td>  537.8959  </td></tr>\n",
       "\t<tr><th scope=row>Cytotoxic lymphocytes</th><td>   41.58387 </td><td>   6.529693 </td><td>   20.730223</td><td>  79.68378  </td><td>  37.48210  </td><td>   40.49905 </td><td>    17.29510</td><td>    99.89621</td><td>   69.86164 </td><td>  210.39135 </td><td>⋯           </td><td>   66.89683 </td><td>  164.70929 </td><td>  12.41965  </td><td>   39.87661 </td><td>   81.40726 </td><td>   89.78837 </td><td>  131.80791 </td><td>   75.51874 </td><td>    74.95644</td><td>  291.7428  </td></tr>\n",
       "\t<tr><th scope=row>NK cells</th><td>   24.13744 </td><td>   5.088166 </td><td>    5.988858</td><td>  25.92171  </td><td>  35.52820  </td><td>   11.17112 </td><td>    22.66280</td><td>    73.33534</td><td>   49.77071 </td><td>   56.60621 </td><td>⋯           </td><td>   32.91442 </td><td>   28.05641 </td><td>  39.41052  </td><td>   55.03378 </td><td>   15.93965 </td><td>   99.74961 </td><td>   81.88579 </td><td>   59.23897 </td><td>    83.26667</td><td>  116.5634  </td></tr>\n",
       "\t<tr><th scope=row>B lineage</th><td>  257.07394 </td><td>  50.423209 </td><td>   51.173434</td><td> 108.10623  </td><td> 120.98494  </td><td>  160.49692 </td><td>    65.32364</td><td>   503.08778</td><td>  308.02022 </td><td> 3976.57277 </td><td>⋯           </td><td>  181.71993 </td><td>  300.57121 </td><td> 130.78001  </td><td>  204.85755 </td><td>   61.03991 </td><td>  790.23599 </td><td> 1065.91892 </td><td>  178.03942 </td><td>   510.20766</td><td>  408.2572  </td></tr>\n",
       "\t<tr><th scope=row>Monocytic lineage</th><td>  703.59358 </td><td>  72.582399 </td><td>  178.045856</td><td> 281.70732  </td><td> 398.72884  </td><td>  577.25072 </td><td>   631.06060</td><td>  1181.59918</td><td> 1053.61526 </td><td> 1570.90034 </td><td>⋯           </td><td> 1120.10784 </td><td>  692.87658 </td><td> 233.31712  </td><td> 1012.37858 </td><td>  573.92779 </td><td> 2873.39554 </td><td> 1851.19389 </td><td> 1001.83503 </td><td>  1750.94157</td><td> 2951.6945  </td></tr>\n",
       "\t<tr><th scope=row>Myeloid dendritic cells</th><td>  106.68688 </td><td>  11.300008 </td><td>   33.141178</td><td>  86.77015  </td><td>  51.25082  </td><td>   33.80558 </td><td>    43.10429</td><td>   230.01630</td><td>  222.03981 </td><td>  199.72563 </td><td>⋯           </td><td>   71.56706 </td><td>   79.20291 </td><td>  90.80000  </td><td>  128.79609 </td><td>   81.20010 </td><td>  161.10536 </td><td>  340.64179 </td><td>  136.37353 </td><td>   173.94844</td><td>  410.6533  </td></tr>\n",
       "\t<tr><th scope=row>Neutrophils</th><td>  659.49477 </td><td> 105.116185 </td><td>  101.384593</td><td> 677.08543  </td><td>1313.08040  </td><td> 1014.35809 </td><td>   506.61231</td><td>  1136.58230</td><td> 1142.73634 </td><td> 1454.25332 </td><td>⋯           </td><td> 1136.78921 </td><td> 1131.13038 </td><td>1130.55919  </td><td> 1140.68556 </td><td>  719.51374 </td><td> 3151.74898 </td><td> 1002.71661 </td><td> 1140.13750 </td><td>  1048.61663</td><td> 2333.4675  </td></tr>\n",
       "\t<tr><th scope=row>Endothelial cells</th><td> 1334.69317 </td><td> 159.916302 </td><td>  322.561283</td><td> 340.47808  </td><td>2242.32781  </td><td> 1609.33176 </td><td>  1947.32990</td><td>  2005.12118</td><td> 2133.78842 </td><td> 2058.15472 </td><td>⋯           </td><td> 1559.55271 </td><td> 1550.30196 </td><td>1034.04410  </td><td> 1806.33275 </td><td>  807.04314 </td><td> 1039.17906 </td><td> 1719.24469 </td><td> 1624.81512 </td><td>  2771.81321</td><td> 2860.8877  </td></tr>\n",
       "\t<tr><th scope=row>Fibroblasts</th><td>17104.38284 </td><td>1613.102243 </td><td>23874.126032</td><td>4953.25464  </td><td>8049.40722  </td><td>16290.57799 </td><td>113795.81921</td><td>121623.82084</td><td>51247.94948 </td><td>57410.96679 </td><td>⋯           </td><td>70305.38662 </td><td>48624.88255 </td><td>7106.69414  </td><td>47844.09478 </td><td>46531.59456 </td><td>92087.02762 </td><td>16565.82265 </td><td>98849.93688 </td><td>131182.85049</td><td>26317.6356  </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllllllllllllllllllllllll}\n",
       "  & gerald.H5NKVBBXX.4.CGGCTATG.TATAGCCT & gerald.H5NKVBBXX.4.CTGAAGCT.ATAGAGGC & gerald.H5NKVBBXX.4.TAATGCGC.ATAGAGGC & gerald.H5NKVBBXX.4.TAATGCGC.TATAGCCT & gerald.H5NKVBBXX.4.TCTCGCGC.ATAGAGGC & gerald.H5NKVBBXX.5.ATTACTCG.ATAGAGGC & gerald.H5NKVBBXX.5.ATTACTCG.CCTATCCT & gerald.H5NKVBBXX.5.ATTACTCG.TATAGCCT & gerald.H5NKVBBXX.5.ATTCAGAA.ATAGAGGC & gerald.H5NKVBBXX.5.CGCTCATT.ATAGAGGC & ⋯ & gerald.H5NKVBBXX.6.TCCGCGAA.ATAGAGGC & gerald.H5NKVBBXX.6.TCCGCGAA.TATAGCCT & gerald.H5NKVBBXX.6.TCTCGCGC.TATAGCCT & gerald.H5NKVBBXX.7.ATTCAGAA.TATAGCCT & gerald.H5NKVBBXX.7.CGCTCATT.TATAGCCT & gerald.H5NKVBBXX.7.CTGAAGCT.TATAGCCT & gerald.H5NKVBBXX.7.GAATTCGT.TATAGCCT & gerald.H5NKVBBXX.7.GAGATTCC.ATAGAGGC & gerald.H5NKVBBXX.7.GAGATTCC.TATAGCCT & gerald.H5NKVBBXX.7.TCCGGAGA.CCTATCCT\\\\\n",
       "\\hline\n",
       "\tT cells &   258.03017  &   42.369740  &    63.672543 &  158.37900   &  565.26341   &   383.62473  &    127.12544 &    512.77558 &   343.97235  &  1190.88239  & ⋯            &   241.35106  &   290.10382  &  252.31332   &   240.35471  &   293.85645  &   369.86630  &   868.87871  &   503.36622  &    423.55900 &   968.3559  \\\\\n",
       "\tCD8 T cells &   128.41972  &    4.993360  &    20.999990 &  229.00000   &  152.95100   &    25.99999  &      0.00000 &    329.00000 &   160.25034  &   232.92266  & ⋯            &   163.30978  &   120.42475  &  178.99980   &   104.09030  &   340.22100  &    76.96831  &   395.32420  &   155.34520  &    154.45260 &   537.8959  \\\\\n",
       "\tCytotoxic lymphocytes &    41.58387  &    6.529693  &    20.730223 &   79.68378   &   37.48210   &    40.49905  &     17.29510 &     99.89621 &    69.86164  &   210.39135  & ⋯            &    66.89683  &   164.70929  &   12.41965   &    39.87661  &    81.40726  &    89.78837  &   131.80791  &    75.51874  &     74.95644 &   291.7428  \\\\\n",
       "\tNK cells &    24.13744  &    5.088166  &     5.988858 &   25.92171   &   35.52820   &    11.17112  &     22.66280 &     73.33534 &    49.77071  &    56.60621  & ⋯            &    32.91442  &    28.05641  &   39.41052   &    55.03378  &    15.93965  &    99.74961  &    81.88579  &    59.23897  &     83.26667 &   116.5634  \\\\\n",
       "\tB lineage &   257.07394  &   50.423209  &    51.173434 &  108.10623   &  120.98494   &   160.49692  &     65.32364 &    503.08778 &   308.02022  &  3976.57277  & ⋯            &   181.71993  &   300.57121  &  130.78001   &   204.85755  &    61.03991  &   790.23599  &  1065.91892  &   178.03942  &    510.20766 &   408.2572  \\\\\n",
       "\tMonocytic lineage &   703.59358  &   72.582399  &   178.045856 &  281.70732   &  398.72884   &   577.25072  &    631.06060 &   1181.59918 &  1053.61526  &  1570.90034  & ⋯            &  1120.10784  &   692.87658  &  233.31712   &  1012.37858  &   573.92779  &  2873.39554  &  1851.19389  &  1001.83503  &   1750.94157 &  2951.6945  \\\\\n",
       "\tMyeloid dendritic cells &   106.68688  &   11.300008  &    33.141178 &   86.77015   &   51.25082   &    33.80558  &     43.10429 &    230.01630 &   222.03981  &   199.72563  & ⋯            &    71.56706  &    79.20291  &   90.80000   &   128.79609  &    81.20010  &   161.10536  &   340.64179  &   136.37353  &    173.94844 &   410.6533  \\\\\n",
       "\tNeutrophils &   659.49477  &  105.116185  &   101.384593 &  677.08543   & 1313.08040   &  1014.35809  &    506.61231 &   1136.58230 &  1142.73634  &  1454.25332  & ⋯            &  1136.78921  &  1131.13038  & 1130.55919   &  1140.68556  &   719.51374  &  3151.74898  &  1002.71661  &  1140.13750  &   1048.61663 &  2333.4675  \\\\\n",
       "\tEndothelial cells &  1334.69317  &  159.916302  &   322.561283 &  340.47808   & 2242.32781   &  1609.33176  &   1947.32990 &   2005.12118 &  2133.78842  &  2058.15472  & ⋯            &  1559.55271  &  1550.30196  & 1034.04410   &  1806.33275  &   807.04314  &  1039.17906  &  1719.24469  &  1624.81512  &   2771.81321 &  2860.8877  \\\\\n",
       "\tFibroblasts & 17104.38284  & 1613.102243  & 23874.126032 & 4953.25464   & 8049.40722   & 16290.57799  & 113795.81921 & 121623.82084 & 51247.94948  & 57410.96679  & ⋯            & 70305.38662  & 48624.88255  & 7106.69414   & 47844.09478  & 46531.59456  & 92087.02762  & 16565.82265  & 98849.93688  & 131182.85049 & 26317.6356  \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | gerald.H5NKVBBXX.4.CGGCTATG.TATAGCCT | gerald.H5NKVBBXX.4.CTGAAGCT.ATAGAGGC | gerald.H5NKVBBXX.4.TAATGCGC.ATAGAGGC | gerald.H5NKVBBXX.4.TAATGCGC.TATAGCCT | gerald.H5NKVBBXX.4.TCTCGCGC.ATAGAGGC | gerald.H5NKVBBXX.5.ATTACTCG.ATAGAGGC | gerald.H5NKVBBXX.5.ATTACTCG.CCTATCCT | gerald.H5NKVBBXX.5.ATTACTCG.TATAGCCT | gerald.H5NKVBBXX.5.ATTCAGAA.ATAGAGGC | gerald.H5NKVBBXX.5.CGCTCATT.ATAGAGGC | ⋯ | gerald.H5NKVBBXX.6.TCCGCGAA.ATAGAGGC | gerald.H5NKVBBXX.6.TCCGCGAA.TATAGCCT | gerald.H5NKVBBXX.6.TCTCGCGC.TATAGCCT | gerald.H5NKVBBXX.7.ATTCAGAA.TATAGCCT | gerald.H5NKVBBXX.7.CGCTCATT.TATAGCCT | gerald.H5NKVBBXX.7.CTGAAGCT.TATAGCCT | gerald.H5NKVBBXX.7.GAATTCGT.TATAGCCT | gerald.H5NKVBBXX.7.GAGATTCC.ATAGAGGC | gerald.H5NKVBBXX.7.GAGATTCC.TATAGCCT | gerald.H5NKVBBXX.7.TCCGGAGA.CCTATCCT | \n",
       "|---|---|---|---|---|---|---|---|---|---|\n",
       "| T cells |   258.03017  |   42.369740  |    63.672543 |  158.37900   |  565.26341   |   383.62473  |    127.12544 |    512.77558 |   343.97235  |  1190.88239  | ⋯            |   241.35106  |   290.10382  |  252.31332   |   240.35471  |   293.85645  |   369.86630  |   868.87871  |   503.36622  |    423.55900 |   968.3559   | \n",
       "| CD8 T cells |   128.41972  |    4.993360  |    20.999990 |  229.00000   |  152.95100   |    25.99999  |      0.00000 |    329.00000 |   160.25034  |   232.92266  | ⋯            |   163.30978  |   120.42475  |  178.99980   |   104.09030  |   340.22100  |    76.96831  |   395.32420  |   155.34520  |    154.45260 |   537.8959   | \n",
       "| Cytotoxic lymphocytes |    41.58387  |    6.529693  |    20.730223 |   79.68378   |   37.48210   |    40.49905  |     17.29510 |     99.89621 |    69.86164  |   210.39135  | ⋯            |    66.89683  |   164.70929  |   12.41965   |    39.87661  |    81.40726  |    89.78837  |   131.80791  |    75.51874  |     74.95644 |   291.7428   | \n",
       "| NK cells |    24.13744  |    5.088166  |     5.988858 |   25.92171   |   35.52820   |    11.17112  |     22.66280 |     73.33534 |    49.77071  |    56.60621  | ⋯            |    32.91442  |    28.05641  |   39.41052   |    55.03378  |    15.93965  |    99.74961  |    81.88579  |    59.23897  |     83.26667 |   116.5634   | \n",
       "| B lineage |   257.07394  |   50.423209  |    51.173434 |  108.10623   |  120.98494   |   160.49692  |     65.32364 |    503.08778 |   308.02022  |  3976.57277  | ⋯            |   181.71993  |   300.57121  |  130.78001   |   204.85755  |    61.03991  |   790.23599  |  1065.91892  |   178.03942  |    510.20766 |   408.2572   | \n",
       "| Monocytic lineage |   703.59358  |   72.582399  |   178.045856 |  281.70732   |  398.72884   |   577.25072  |    631.06060 |   1181.59918 |  1053.61526  |  1570.90034  | ⋯            |  1120.10784  |   692.87658  |  233.31712   |  1012.37858  |   573.92779  |  2873.39554  |  1851.19389  |  1001.83503  |   1750.94157 |  2951.6945   | \n",
       "| Myeloid dendritic cells |   106.68688  |   11.300008  |    33.141178 |   86.77015   |   51.25082   |    33.80558  |     43.10429 |    230.01630 |   222.03981  |   199.72563  | ⋯            |    71.56706  |    79.20291  |   90.80000   |   128.79609  |    81.20010  |   161.10536  |   340.64179  |   136.37353  |    173.94844 |   410.6533   | \n",
       "| Neutrophils |   659.49477  |  105.116185  |   101.384593 |  677.08543   | 1313.08040   |  1014.35809  |    506.61231 |   1136.58230 |  1142.73634  |  1454.25332  | ⋯            |  1136.78921  |  1131.13038  | 1130.55919   |  1140.68556  |   719.51374  |  3151.74898  |  1002.71661  |  1140.13750  |   1048.61663 |  2333.4675   | \n",
       "| Endothelial cells |  1334.69317  |  159.916302  |   322.561283 |  340.47808   | 2242.32781   |  1609.33176  |   1947.32990 |   2005.12118 |  2133.78842  |  2058.15472  | ⋯            |  1559.55271  |  1550.30196  | 1034.04410   |  1806.33275  |   807.04314  |  1039.17906  |  1719.24469  |  1624.81512  |   2771.81321 |  2860.8877   | \n",
       "| Fibroblasts | 17104.38284  | 1613.102243  | 23874.126032 | 4953.25464   | 8049.40722   | 16290.57799  | 113795.81921 | 121623.82084 | 51247.94948  | 57410.96679  | ⋯            | 70305.38662  | 48624.88255  | 7106.69414   | 47844.09478  | 46531.59456  | 92087.02762  | 16565.82265  | 98849.93688  | 131182.85049 | 26317.6356   | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "                        gerald.H5NKVBBXX.4.CGGCTATG.TATAGCCT\n",
       "T cells                   258.03017                         \n",
       "CD8 T cells               128.41972                         \n",
       "Cytotoxic lymphocytes      41.58387                         \n",
       "NK cells                   24.13744                         \n",
       "B lineage                 257.07394                         \n",
       "Monocytic lineage         703.59358                         \n",
       "Myeloid dendritic cells   106.68688                         \n",
       "Neutrophils               659.49477                         \n",
       "Endothelial cells        1334.69317                         \n",
       "Fibroblasts             17104.38284                         \n",
       "                        gerald.H5NKVBBXX.4.CTGAAGCT.ATAGAGGC\n",
       "T cells                   42.369740                         \n",
       "CD8 T cells                4.993360                         \n",
       "Cytotoxic lymphocytes      6.529693                         \n",
       "NK cells                   5.088166                         \n",
       "B lineage                 50.423209                         \n",
       "Monocytic lineage         72.582399                         \n",
       "Myeloid dendritic cells   11.300008                         \n",
       "Neutrophils              105.116185                         \n",
       "Endothelial cells        159.916302                         \n",
       "Fibroblasts             1613.102243                         \n",
       "                        gerald.H5NKVBBXX.4.TAATGCGC.ATAGAGGC\n",
       "T cells                    63.672543                        \n",
       "CD8 T cells                20.999990                        \n",
       "Cytotoxic lymphocytes      20.730223                        \n",
       "NK cells                    5.988858                        \n",
       "B lineage                  51.173434                        \n",
       "Monocytic lineage         178.045856                        \n",
       "Myeloid dendritic cells    33.141178                        \n",
       "Neutrophils               101.384593                        \n",
       "Endothelial cells         322.561283                        \n",
       "Fibroblasts             23874.126032                        \n",
       "                        gerald.H5NKVBBXX.4.TAATGCGC.TATAGCCT\n",
       "T cells                  158.37900                          \n",
       "CD8 T cells              229.00000                          \n",
       "Cytotoxic lymphocytes     79.68378                          \n",
       "NK cells                  25.92171                          \n",
       "B lineage                108.10623                          \n",
       "Monocytic lineage        281.70732                          \n",
       "Myeloid dendritic cells   86.77015                          \n",
       "Neutrophils              677.08543                          \n",
       "Endothelial cells        340.47808                          \n",
       "Fibroblasts             4953.25464                          \n",
       "                        gerald.H5NKVBBXX.4.TCTCGCGC.ATAGAGGC\n",
       "T cells                  565.26341                          \n",
       "CD8 T cells              152.95100                          \n",
       "Cytotoxic lymphocytes     37.48210                          \n",
       "NK cells                  35.52820                          \n",
       "B lineage                120.98494                          \n",
       "Monocytic lineage        398.72884                          \n",
       "Myeloid dendritic cells   51.25082                          \n",
       "Neutrophils             1313.08040                          \n",
       "Endothelial cells       2242.32781                          \n",
       "Fibroblasts             8049.40722                          \n",
       "                        gerald.H5NKVBBXX.5.ATTACTCG.ATAGAGGC\n",
       "T cells                   383.62473                         \n",
       "CD8 T cells                25.99999                         \n",
       "Cytotoxic lymphocytes      40.49905                         \n",
       "NK cells                   11.17112                         \n",
       "B lineage                 160.49692                         \n",
       "Monocytic lineage         577.25072                         \n",
       "Myeloid dendritic cells    33.80558                         \n",
       "Neutrophils              1014.35809                         \n",
       "Endothelial cells        1609.33176                         \n",
       "Fibroblasts             16290.57799                         \n",
       "                        gerald.H5NKVBBXX.5.ATTACTCG.CCTATCCT\n",
       "T cells                    127.12544                        \n",
       "CD8 T cells                  0.00000                        \n",
       "Cytotoxic lymphocytes       17.29510                        \n",
       "NK cells                    22.66280                        \n",
       "B lineage                   65.32364                        \n",
       "Monocytic lineage          631.06060                        \n",
       "Myeloid dendritic cells     43.10429                        \n",
       "Neutrophils                506.61231                        \n",
       "Endothelial cells         1947.32990                        \n",
       "Fibroblasts             113795.81921                        \n",
       "                        gerald.H5NKVBBXX.5.ATTACTCG.TATAGCCT\n",
       "T cells                    512.77558                        \n",
       "CD8 T cells                329.00000                        \n",
       "Cytotoxic lymphocytes       99.89621                        \n",
       "NK cells                    73.33534                        \n",
       "B lineage                  503.08778                        \n",
       "Monocytic lineage         1181.59918                        \n",
       "Myeloid dendritic cells    230.01630                        \n",
       "Neutrophils               1136.58230                        \n",
       "Endothelial cells         2005.12118                        \n",
       "Fibroblasts             121623.82084                        \n",
       "                        gerald.H5NKVBBXX.5.ATTCAGAA.ATAGAGGC\n",
       "T cells                   343.97235                         \n",
       "CD8 T cells               160.25034                         \n",
       "Cytotoxic lymphocytes      69.86164                         \n",
       "NK cells                   49.77071                         \n",
       "B lineage                 308.02022                         \n",
       "Monocytic lineage        1053.61526                         \n",
       "Myeloid dendritic cells   222.03981                         \n",
       "Neutrophils              1142.73634                         \n",
       "Endothelial cells        2133.78842                         \n",
       "Fibroblasts             51247.94948                         \n",
       "                        gerald.H5NKVBBXX.5.CGCTCATT.ATAGAGGC ⋯\n",
       "T cells                  1190.88239                          ⋯\n",
       "CD8 T cells               232.92266                          ⋯\n",
       "Cytotoxic lymphocytes     210.39135                          ⋯\n",
       "NK cells                   56.60621                          ⋯\n",
       "B lineage                3976.57277                          ⋯\n",
       "Monocytic lineage        1570.90034                          ⋯\n",
       "Myeloid dendritic cells   199.72563                          ⋯\n",
       "Neutrophils              1454.25332                          ⋯\n",
       "Endothelial cells        2058.15472                          ⋯\n",
       "Fibroblasts             57410.96679                          ⋯\n",
       "                        gerald.H5NKVBBXX.6.TCCGCGAA.ATAGAGGC\n",
       "T cells                   241.35106                         \n",
       "CD8 T cells               163.30978                         \n",
       "Cytotoxic lymphocytes      66.89683                         \n",
       "NK cells                   32.91442                         \n",
       "B lineage                 181.71993                         \n",
       "Monocytic lineage        1120.10784                         \n",
       "Myeloid dendritic cells    71.56706                         \n",
       "Neutrophils              1136.78921                         \n",
       "Endothelial cells        1559.55271                         \n",
       "Fibroblasts             70305.38662                         \n",
       "                        gerald.H5NKVBBXX.6.TCCGCGAA.TATAGCCT\n",
       "T cells                   290.10382                         \n",
       "CD8 T cells               120.42475                         \n",
       "Cytotoxic lymphocytes     164.70929                         \n",
       "NK cells                   28.05641                         \n",
       "B lineage                 300.57121                         \n",
       "Monocytic lineage         692.87658                         \n",
       "Myeloid dendritic cells    79.20291                         \n",
       "Neutrophils              1131.13038                         \n",
       "Endothelial cells        1550.30196                         \n",
       "Fibroblasts             48624.88255                         \n",
       "                        gerald.H5NKVBBXX.6.TCTCGCGC.TATAGCCT\n",
       "T cells                  252.31332                          \n",
       "CD8 T cells              178.99980                          \n",
       "Cytotoxic lymphocytes     12.41965                          \n",
       "NK cells                  39.41052                          \n",
       "B lineage                130.78001                          \n",
       "Monocytic lineage        233.31712                          \n",
       "Myeloid dendritic cells   90.80000                          \n",
       "Neutrophils             1130.55919                          \n",
       "Endothelial cells       1034.04410                          \n",
       "Fibroblasts             7106.69414                          \n",
       "                        gerald.H5NKVBBXX.7.ATTCAGAA.TATAGCCT\n",
       "T cells                   240.35471                         \n",
       "CD8 T cells               104.09030                         \n",
       "Cytotoxic lymphocytes      39.87661                         \n",
       "NK cells                   55.03378                         \n",
       "B lineage                 204.85755                         \n",
       "Monocytic lineage        1012.37858                         \n",
       "Myeloid dendritic cells   128.79609                         \n",
       "Neutrophils              1140.68556                         \n",
       "Endothelial cells        1806.33275                         \n",
       "Fibroblasts             47844.09478                         \n",
       "                        gerald.H5NKVBBXX.7.CGCTCATT.TATAGCCT\n",
       "T cells                   293.85645                         \n",
       "CD8 T cells               340.22100                         \n",
       "Cytotoxic lymphocytes      81.40726                         \n",
       "NK cells                   15.93965                         \n",
       "B lineage                  61.03991                         \n",
       "Monocytic lineage         573.92779                         \n",
       "Myeloid dendritic cells    81.20010                         \n",
       "Neutrophils               719.51374                         \n",
       "Endothelial cells         807.04314                         \n",
       "Fibroblasts             46531.59456                         \n",
       "                        gerald.H5NKVBBXX.7.CTGAAGCT.TATAGCCT\n",
       "T cells                   369.86630                         \n",
       "CD8 T cells                76.96831                         \n",
       "Cytotoxic lymphocytes      89.78837                         \n",
       "NK cells                   99.74961                         \n",
       "B lineage                 790.23599                         \n",
       "Monocytic lineage        2873.39554                         \n",
       "Myeloid dendritic cells   161.10536                         \n",
       "Neutrophils              3151.74898                         \n",
       "Endothelial cells        1039.17906                         \n",
       "Fibroblasts             92087.02762                         \n",
       "                        gerald.H5NKVBBXX.7.GAATTCGT.TATAGCCT\n",
       "T cells                   868.87871                         \n",
       "CD8 T cells               395.32420                         \n",
       "Cytotoxic lymphocytes     131.80791                         \n",
       "NK cells                   81.88579                         \n",
       "B lineage                1065.91892                         \n",
       "Monocytic lineage        1851.19389                         \n",
       "Myeloid dendritic cells   340.64179                         \n",
       "Neutrophils              1002.71661                         \n",
       "Endothelial cells        1719.24469                         \n",
       "Fibroblasts             16565.82265                         \n",
       "                        gerald.H5NKVBBXX.7.GAGATTCC.ATAGAGGC\n",
       "T cells                   503.36622                         \n",
       "CD8 T cells               155.34520                         \n",
       "Cytotoxic lymphocytes      75.51874                         \n",
       "NK cells                   59.23897                         \n",
       "B lineage                 178.03942                         \n",
       "Monocytic lineage        1001.83503                         \n",
       "Myeloid dendritic cells   136.37353                         \n",
       "Neutrophils              1140.13750                         \n",
       "Endothelial cells        1624.81512                         \n",
       "Fibroblasts             98849.93688                         \n",
       "                        gerald.H5NKVBBXX.7.GAGATTCC.TATAGCCT\n",
       "T cells                    423.55900                        \n",
       "CD8 T cells                154.45260                        \n",
       "Cytotoxic lymphocytes       74.95644                        \n",
       "NK cells                    83.26667                        \n",
       "B lineage                  510.20766                        \n",
       "Monocytic lineage         1750.94157                        \n",
       "Myeloid dendritic cells    173.94844                        \n",
       "Neutrophils               1048.61663                        \n",
       "Endothelial cells         2771.81321                        \n",
       "Fibroblasts             131182.85049                        \n",
       "                        gerald.H5NKVBBXX.7.TCCGGAGA.CCTATCCT\n",
       "T cells                   968.3559                          \n",
       "CD8 T cells               537.8959                          \n",
       "Cytotoxic lymphocytes     291.7428                          \n",
       "NK cells                  116.5634                          \n",
       "B lineage                 408.2572                          \n",
       "Monocytic lineage        2951.6945                          \n",
       "Myeloid dendritic cells   410.6533                          \n",
       "Neutrophils              2333.4675                          \n",
       "Endothelial cells        2860.8877                          \n",
       "Fibroblasts             26317.6356                          "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "tmpdir <- \"build\"\n",
    "expression_data <- get_expression_data(tmpdir)\n",
    "head3(expression_data)\n",
    "# run_cibersort(expression_data, tmpdir)\n",
    "# run_estimate(expression_data %>% data.frame() %>% tibble::column_to_rownames('Gene_symbol'), tmpdir)\n",
    "# run_estimate(expression_data, tmpdir)\n",
    "# run_xcell(expression_data, tmpdir)\n",
    "run_mcpcounter(expression_data, tmpdir)"
   ]
  }
 ],
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