figure3_04_normal-vs-cancer_enhancers.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "c643ff42",
   "metadata": {},
   "source": [
    "# load library"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "359e7eda",
   "metadata": {},
   "outputs": [],
   "source": [
    "source(\"r/jupyter_common.R\")\n",
    "source(\"r/identify_cell_types.R\")\n",
    "source(\"r/plot_sc_clusters.R\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "016b237a",
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "# data structure\n",
    "suppressPackageStartupMessages(library(data.table))\n",
    "\n",
    "# single cell analysis\n",
    "suppressPackageStartupMessages(library(Seurat))\n",
    "suppressPackageStartupMessages(library(ArchR))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7e717b79",
   "metadata": {},
   "source": [
    "# parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "699a8430",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'RNA_harmony_th.0'"
      ],
      "text/latex": [
       "'RNA\\_harmony\\_th.0'"
      ],
      "text/markdown": [
       "'RNA_harmony_th.0'"
      ],
      "text/plain": [
       "[1] \"RNA_harmony_th.0\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "'umapharmony'"
      ],
      "text/latex": [
       "'umapharmony'"
      ],
      "text/markdown": [
       "'umapharmony'"
      ],
      "text/plain": [
       "[1] \"umapharmony\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "'cluster.type.harmony'"
      ],
      "text/latex": [
       "'cluster.type.harmony'"
      ],
      "text/markdown": [
       "'cluster.type.harmony'"
      ],
      "text/plain": [
       "[1] \"cluster.type.harmony\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "str_condition <- \"male-bc\"\n",
    "\n",
    "args <- list()\n",
    "args$cancer_type <- \"male-bc\"\n",
    "args$harmony_theta <- 0\n",
    "str_column_of_meta_data_harmony <- sprintf(\"RNA_harmony_th.%s\", paste(args$harmony_theta, collapse=\",\"))\n",
    "\n",
    "str_reduction <- \"pca\"\n",
    "str_umap_reduction <- \"umap\"  \n",
    "col_cluster_types <- \"cluster.type\"\n",
    "\n",
    "if (args$harmony_theta >= 0) {\n",
    "    str_column_of_meta_data_cluster <- str_column_of_meta_data_harmony\n",
    "    str_reduction <- \"harmony\"\n",
    "    str_umap_reduction <- \"umapharmony\"\n",
    "    col_cluster_types <- \"cluster.type.harmony\"\n",
    "}\n",
    "\n",
    "\n",
    "str_column_of_meta_data_cluster\n",
    "str_umap_reduction\n",
    "col_cluster_types\n",
    "\n",
    "\n",
    "figure_format <- \"pdf\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3119ef41",
   "metadata": {},
   "source": [
    "## set.seed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "a004738e",
   "metadata": {},
   "outputs": [],
   "source": [
    "# set seed for reproducibility\n",
    "set.seed(51)\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "291e5b63",
   "metadata": {},
   "source": [
    "## display"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "eabb56a4",
   "metadata": {},
   "outputs": [],
   "source": [
    "options(repr.matrix.max.cols=150, repr.matrix.max.rows=50)\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "56ef227f",
   "metadata": {},
   "source": [
    "# read scRNA-seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "e6c782ec",
   "metadata": {},
   "outputs": [],
   "source": [
    "dir_rna <- \"/home/hkim77/francolab.w/sc-rna-seq/male-bc/run-20220725\"\n",
    "fname_rna <- sprintf(\"%s/output_male-bc/rds_male-bc/male-bc_sc-rna-seq_merged_seurat_obj.rds\", dir_rna)\n",
    "\n",
    "rna <- readRDS(fname_rna)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "815aaf92",
   "metadata": {},
   "source": [
    "## pattern_cluster.type_removal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "f6fb1eea",
   "metadata": {},
   "outputs": [],
   "source": [
    "pattern_cluster.type_removal <- \"1-|6-|8-\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "62e73c23",
   "metadata": {},
   "source": [
    "## rna$type_normal_cancer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "e6f91faa",
   "metadata": {},
   "outputs": [],
   "source": [
    "vec_cluster_types <- rna@meta.data[,col_cluster_types]\n",
    "#table(vec_cluster_types)\n",
    "rna$type_normal_cancer <- \"Normal\"\n",
    "rna$type_normal_cancer[grepl(\"Epi\", vec_cluster_types)] <- \"Cancer\"\n",
    "rna$type_normal_cancer <- factor(rna$type_normal_cancer, level=c(\"Normal\", \"Cancer\"))\n",
    "\n",
    "# exclude\n",
    "f.exclude <- grepl(pattern_cluster.type_removal, vec_cluster_types)\n",
    "rna$type_normal_cancer[f.exclude] <- NA\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "faf226fd",
   "metadata": {},
   "source": [
    "# read scATAC-seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "189a2838",
   "metadata": {},
   "outputs": [],
   "source": [
    "dir_atac <- \"/home/hkim77/francolab.w/sc-atac-seq/male-bc/run-20220725\"\n",
    "dir_output <- sprintf(\"%s/output_male-bc\", dir_atac)\n",
    "dir_output_p2g <- sprintf(\"%s/output_p2g_male-bc\", dir_atac)\n",
    "fname_atac <- sprintf(\"%s/rds/male-bc_archrproj_obj_final.rds\", dir_output)\n",
    "\n",
    "atac <- readRDS(fname_atac)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d51b84a6",
   "metadata": {},
   "source": [
    "# normal vs. cancer"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "18cce0c4",
   "metadata": {},
   "source": [
    "## df_p2g"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "cfcc4127",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A data.frame: 6 × 13</caption>\n",
       "<thead>\n",
       "\t<tr><th></th><th scope=col>idxATAC</th><th scope=col>idxRNA</th><th scope=col>Correlation</th><th scope=col>FDR</th><th scope=col>VarQATAC</th><th scope=col>VarQRNA</th><th scope=col>EmpPval</th><th scope=col>EmpFDR</th><th scope=col>geneName</th><th scope=col>peakName</th><th scope=col>peakType</th><th scope=col>idx</th><th scope=col>kmeans</th></tr>\n",
       "\t<tr><th></th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>1</th><td>29</td><td>3</td><td>0.5394961</td><td> 6.024423e-38</td><td>0.9396097</td><td>0.4338114</td><td>0.11278982</td><td>0.7965846</td><td>FAM41C </td><td>chr1:1079324-1079824</td><td>Distal</td><td>29-3</td><td>3</td></tr>\n",
       "\t<tr><th scope=row>2</th><td>24</td><td>7</td><td>0.7894052</td><td>5.401495e-105</td><td>0.7539227</td><td>0.5385226</td><td>0.01994288</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1068557-1069057</td><td>Distal</td><td>24-7</td><td>3</td></tr>\n",
       "\t<tr><th scope=row>3</th><td>25</td><td>7</td><td>0.7349978</td><td> 6.699672e-84</td><td>0.7787057</td><td>0.5385226</td><td>0.03031435</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1069078-1069578</td><td>Distal</td><td>25-7</td><td>3</td></tr>\n",
       "\t<tr><th scope=row>4</th><td>26</td><td>7</td><td>0.8462787</td><td>5.132060e-135</td><td>0.7508486</td><td>0.5385226</td><td>0.01255312</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1069752-1070252</td><td>Distal</td><td>26-7</td><td>3</td></tr>\n",
       "\t<tr><th scope=row>5</th><td>29</td><td>7</td><td>0.8539726</td><td>5.278697e-140</td><td>0.9396097</td><td>0.5385226</td><td>0.01176771</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1079324-1079824</td><td>Distal</td><td>29-7</td><td>3</td></tr>\n",
       "\t<tr><th scope=row>6</th><td>30</td><td>7</td><td>0.6868139</td><td> 3.617362e-69</td><td>0.4759030</td><td>0.5385226</td><td>0.04307672</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1080052-1080552</td><td>Distal</td><td>30-7</td><td>3</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.frame: 6 × 13\n",
       "\\begin{tabular}{r|lllllllllllll}\n",
       "  & idxATAC & idxRNA & Correlation & FDR & VarQATAC & VarQRNA & EmpPval & EmpFDR & geneName & peakName & peakType & idx & kmeans\\\\\n",
       "  & <int> & <int> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <chr> & <chr> & <chr> & <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t1 & 29 & 3 & 0.5394961 &  6.024423e-38 & 0.9396097 & 0.4338114 & 0.11278982 & 0.7965846 & FAM41C  & chr1:1079324-1079824 & Distal & 29-3 & 3\\\\\n",
       "\t2 & 24 & 7 & 0.7894052 & 5.401495e-105 & 0.7539227 & 0.5385226 & 0.01994288 & 0.7892789 & PLEKHN1 & chr1:1068557-1069057 & Distal & 24-7 & 3\\\\\n",
       "\t3 & 25 & 7 & 0.7349978 &  6.699672e-84 & 0.7787057 & 0.5385226 & 0.03031435 & 0.7892789 & PLEKHN1 & chr1:1069078-1069578 & Distal & 25-7 & 3\\\\\n",
       "\t4 & 26 & 7 & 0.8462787 & 5.132060e-135 & 0.7508486 & 0.5385226 & 0.01255312 & 0.7892789 & PLEKHN1 & chr1:1069752-1070252 & Distal & 26-7 & 3\\\\\n",
       "\t5 & 29 & 7 & 0.8539726 & 5.278697e-140 & 0.9396097 & 0.5385226 & 0.01176771 & 0.7892789 & PLEKHN1 & chr1:1079324-1079824 & Distal & 29-7 & 3\\\\\n",
       "\t6 & 30 & 7 & 0.6868139 &  3.617362e-69 & 0.4759030 & 0.5385226 & 0.04307672 & 0.7892789 & PLEKHN1 & chr1:1080052-1080552 & Distal & 30-7 & 3\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.frame: 6 × 13\n",
       "\n",
       "| <!--/--> | idxATAC &lt;int&gt; | idxRNA &lt;int&gt; | Correlation &lt;dbl&gt; | FDR &lt;dbl&gt; | VarQATAC &lt;dbl&gt; | VarQRNA &lt;dbl&gt; | EmpPval &lt;dbl&gt; | EmpFDR &lt;dbl&gt; | geneName &lt;chr&gt; | peakName &lt;chr&gt; | peakType &lt;chr&gt; | idx &lt;chr&gt; | kmeans &lt;int&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| 1 | 29 | 3 | 0.5394961 |  6.024423e-38 | 0.9396097 | 0.4338114 | 0.11278982 | 0.7965846 | FAM41C  | chr1:1079324-1079824 | Distal | 29-3 | 3 |\n",
       "| 2 | 24 | 7 | 0.7894052 | 5.401495e-105 | 0.7539227 | 0.5385226 | 0.01994288 | 0.7892789 | PLEKHN1 | chr1:1068557-1069057 | Distal | 24-7 | 3 |\n",
       "| 3 | 25 | 7 | 0.7349978 |  6.699672e-84 | 0.7787057 | 0.5385226 | 0.03031435 | 0.7892789 | PLEKHN1 | chr1:1069078-1069578 | Distal | 25-7 | 3 |\n",
       "| 4 | 26 | 7 | 0.8462787 | 5.132060e-135 | 0.7508486 | 0.5385226 | 0.01255312 | 0.7892789 | PLEKHN1 | chr1:1069752-1070252 | Distal | 26-7 | 3 |\n",
       "| 5 | 29 | 7 | 0.8539726 | 5.278697e-140 | 0.9396097 | 0.5385226 | 0.01176771 | 0.7892789 | PLEKHN1 | chr1:1079324-1079824 | Distal | 29-7 | 3 |\n",
       "| 6 | 30 | 7 | 0.6868139 |  3.617362e-69 | 0.4759030 | 0.5385226 | 0.04307672 | 0.7892789 | PLEKHN1 | chr1:1080052-1080552 | Distal | 30-7 | 3 |\n",
       "\n"
      ],
      "text/plain": [
       "  idxATAC idxRNA Correlation FDR           VarQATAC  VarQRNA   EmpPval   \n",
       "1 29      3      0.5394961    6.024423e-38 0.9396097 0.4338114 0.11278982\n",
       "2 24      7      0.7894052   5.401495e-105 0.7539227 0.5385226 0.01994288\n",
       "3 25      7      0.7349978    6.699672e-84 0.7787057 0.5385226 0.03031435\n",
       "4 26      7      0.8462787   5.132060e-135 0.7508486 0.5385226 0.01255312\n",
       "5 29      7      0.8539726   5.278697e-140 0.9396097 0.5385226 0.01176771\n",
       "6 30      7      0.6868139    3.617362e-69 0.4759030 0.5385226 0.04307672\n",
       "  EmpFDR    geneName peakName             peakType idx  kmeans\n",
       "1 0.7965846 FAM41C   chr1:1079324-1079824 Distal   29-3 3     \n",
       "2 0.7892789 PLEKHN1  chr1:1068557-1069057 Distal   24-7 3     \n",
       "3 0.7892789 PLEKHN1  chr1:1069078-1069578 Distal   25-7 3     \n",
       "4 0.7892789 PLEKHN1  chr1:1069752-1070252 Distal   26-7 3     \n",
       "5 0.7892789 PLEKHN1  chr1:1079324-1079824 Distal   29-7 3     \n",
       "6 0.7892789 PLEKHN1  chr1:1080052-1080552 Distal   30-7 3     "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>22869</li><li>13</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 22869\n",
       "\\item 13\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 22869\n",
       "2. 13\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 22869    13"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# unique peaks_p2g: 11719\n",
      "# unique genes: 7353\n"
     ]
    }
   ],
   "source": [
    "peaktype <- \"enhancer\"\n",
    "\n",
    "# all p2g\n",
    "fname_rds <- sprintf(\"%s/rds/p2g.df.sub.plot_%s.rds\", dir_output_p2g, peaktype)\n",
    "filename_appendix <- \"\"\n",
    "\n",
    "df_p2g <- readRDS(fname_rds)\n",
    "head(df_p2g)\n",
    "dim(df_p2g)\n",
    "\n",
    "peaks_p2g <- unique(df_p2g$peakName)\n",
    "n_upeaks_p2g <- length(peaks_p2g)\n",
    "\n",
    "genes_p2g <- unique(df_p2g$geneName)\n",
    "n_ugenes_p2g <- length(genes_p2g)\n",
    "\n",
    "cat(sprintf(\"# unique peaks_p2g: %d\\n\", n_upeaks_p2g))\n",
    "cat(sprintf(\"# unique genes: %d\\n\", n_ugenes_p2g))\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ec1cdfab",
   "metadata": {},
   "source": [
    "## df_p2g_epi"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "acdaffbe",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A data.frame: 6 × 13</caption>\n",
       "<thead>\n",
       "\t<tr><th></th><th scope=col>idxATAC</th><th scope=col>idxRNA</th><th scope=col>Correlation</th><th scope=col>FDR</th><th scope=col>VarQATAC</th><th scope=col>VarQRNA</th><th scope=col>EmpPval</th><th scope=col>EmpFDR</th><th scope=col>geneName</th><th scope=col>peakName</th><th scope=col>peakType</th><th scope=col>idx</th><th scope=col>kmeans</th></tr>\n",
       "\t<tr><th></th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>1</th><td>29</td><td>3</td><td>0.5394961</td><td> 6.024423e-38</td><td>0.9396097</td><td>0.4338114</td><td>0.11278982</td><td>0.7965846</td><td>FAM41C </td><td>chr1:1079324-1079824</td><td>Distal</td><td>29-3</td><td>3</td></tr>\n",
       "\t<tr><th scope=row>2</th><td>24</td><td>7</td><td>0.7894052</td><td>5.401495e-105</td><td>0.7539227</td><td>0.5385226</td><td>0.01994288</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1068557-1069057</td><td>Distal</td><td>24-7</td><td>3</td></tr>\n",
       "\t<tr><th scope=row>3</th><td>25</td><td>7</td><td>0.7349978</td><td> 6.699672e-84</td><td>0.7787057</td><td>0.5385226</td><td>0.03031435</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1069078-1069578</td><td>Distal</td><td>25-7</td><td>3</td></tr>\n",
       "\t<tr><th scope=row>4</th><td>26</td><td>7</td><td>0.8462787</td><td>5.132060e-135</td><td>0.7508486</td><td>0.5385226</td><td>0.01255312</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1069752-1070252</td><td>Distal</td><td>26-7</td><td>3</td></tr>\n",
       "\t<tr><th scope=row>5</th><td>29</td><td>7</td><td>0.8539726</td><td>5.278697e-140</td><td>0.9396097</td><td>0.5385226</td><td>0.01176771</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1079324-1079824</td><td>Distal</td><td>29-7</td><td>3</td></tr>\n",
       "\t<tr><th scope=row>6</th><td>30</td><td>7</td><td>0.6868139</td><td> 3.617362e-69</td><td>0.4759030</td><td>0.5385226</td><td>0.04307672</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1080052-1080552</td><td>Distal</td><td>30-7</td><td>3</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.frame: 6 × 13\n",
       "\\begin{tabular}{r|lllllllllllll}\n",
       "  & idxATAC & idxRNA & Correlation & FDR & VarQATAC & VarQRNA & EmpPval & EmpFDR & geneName & peakName & peakType & idx & kmeans\\\\\n",
       "  & <int> & <int> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <chr> & <chr> & <chr> & <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t1 & 29 & 3 & 0.5394961 &  6.024423e-38 & 0.9396097 & 0.4338114 & 0.11278982 & 0.7965846 & FAM41C  & chr1:1079324-1079824 & Distal & 29-3 & 3\\\\\n",
       "\t2 & 24 & 7 & 0.7894052 & 5.401495e-105 & 0.7539227 & 0.5385226 & 0.01994288 & 0.7892789 & PLEKHN1 & chr1:1068557-1069057 & Distal & 24-7 & 3\\\\\n",
       "\t3 & 25 & 7 & 0.7349978 &  6.699672e-84 & 0.7787057 & 0.5385226 & 0.03031435 & 0.7892789 & PLEKHN1 & chr1:1069078-1069578 & Distal & 25-7 & 3\\\\\n",
       "\t4 & 26 & 7 & 0.8462787 & 5.132060e-135 & 0.7508486 & 0.5385226 & 0.01255312 & 0.7892789 & PLEKHN1 & chr1:1069752-1070252 & Distal & 26-7 & 3\\\\\n",
       "\t5 & 29 & 7 & 0.8539726 & 5.278697e-140 & 0.9396097 & 0.5385226 & 0.01176771 & 0.7892789 & PLEKHN1 & chr1:1079324-1079824 & Distal & 29-7 & 3\\\\\n",
       "\t6 & 30 & 7 & 0.6868139 &  3.617362e-69 & 0.4759030 & 0.5385226 & 0.04307672 & 0.7892789 & PLEKHN1 & chr1:1080052-1080552 & Distal & 30-7 & 3\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.frame: 6 × 13\n",
       "\n",
       "| <!--/--> | idxATAC &lt;int&gt; | idxRNA &lt;int&gt; | Correlation &lt;dbl&gt; | FDR &lt;dbl&gt; | VarQATAC &lt;dbl&gt; | VarQRNA &lt;dbl&gt; | EmpPval &lt;dbl&gt; | EmpFDR &lt;dbl&gt; | geneName &lt;chr&gt; | peakName &lt;chr&gt; | peakType &lt;chr&gt; | idx &lt;chr&gt; | kmeans &lt;int&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| 1 | 29 | 3 | 0.5394961 |  6.024423e-38 | 0.9396097 | 0.4338114 | 0.11278982 | 0.7965846 | FAM41C  | chr1:1079324-1079824 | Distal | 29-3 | 3 |\n",
       "| 2 | 24 | 7 | 0.7894052 | 5.401495e-105 | 0.7539227 | 0.5385226 | 0.01994288 | 0.7892789 | PLEKHN1 | chr1:1068557-1069057 | Distal | 24-7 | 3 |\n",
       "| 3 | 25 | 7 | 0.7349978 |  6.699672e-84 | 0.7787057 | 0.5385226 | 0.03031435 | 0.7892789 | PLEKHN1 | chr1:1069078-1069578 | Distal | 25-7 | 3 |\n",
       "| 4 | 26 | 7 | 0.8462787 | 5.132060e-135 | 0.7508486 | 0.5385226 | 0.01255312 | 0.7892789 | PLEKHN1 | chr1:1069752-1070252 | Distal | 26-7 | 3 |\n",
       "| 5 | 29 | 7 | 0.8539726 | 5.278697e-140 | 0.9396097 | 0.5385226 | 0.01176771 | 0.7892789 | PLEKHN1 | chr1:1079324-1079824 | Distal | 29-7 | 3 |\n",
       "| 6 | 30 | 7 | 0.6868139 |  3.617362e-69 | 0.4759030 | 0.5385226 | 0.04307672 | 0.7892789 | PLEKHN1 | chr1:1080052-1080552 | Distal | 30-7 | 3 |\n",
       "\n"
      ],
      "text/plain": [
       "  idxATAC idxRNA Correlation FDR           VarQATAC  VarQRNA   EmpPval   \n",
       "1 29      3      0.5394961    6.024423e-38 0.9396097 0.4338114 0.11278982\n",
       "2 24      7      0.7894052   5.401495e-105 0.7539227 0.5385226 0.01994288\n",
       "3 25      7      0.7349978    6.699672e-84 0.7787057 0.5385226 0.03031435\n",
       "4 26      7      0.8462787   5.132060e-135 0.7508486 0.5385226 0.01255312\n",
       "5 29      7      0.8539726   5.278697e-140 0.9396097 0.5385226 0.01176771\n",
       "6 30      7      0.6868139    3.617362e-69 0.4759030 0.5385226 0.04307672\n",
       "  EmpFDR    geneName peakName             peakType idx  kmeans\n",
       "1 0.7965846 FAM41C   chr1:1079324-1079824 Distal   29-3 3     \n",
       "2 0.7892789 PLEKHN1  chr1:1068557-1069057 Distal   24-7 3     \n",
       "3 0.7892789 PLEKHN1  chr1:1069078-1069578 Distal   25-7 3     \n",
       "4 0.7892789 PLEKHN1  chr1:1069752-1070252 Distal   26-7 3     \n",
       "5 0.7892789 PLEKHN1  chr1:1079324-1079824 Distal   29-7 3     \n",
       "6 0.7892789 PLEKHN1  chr1:1080052-1080552 Distal   30-7 3     "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>15275</li><li>13</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 15275\n",
       "\\item 13\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 15275\n",
       "2. 13\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 15275    13"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# unique peaks epi: 6790\n",
      "# unique genes epi: 3939\n"
     ]
    }
   ],
   "source": [
    "peaktype <- \"enhancer\"\n",
    "\n",
    "# all epithelial cells\n",
    "fname_rds <- sprintf(\"%s/rds/cancer_enriched_%s_p2g_table.rds\", dir_output_p2g, peaktype)\n",
    "\n",
    "df_p2g_epi <- readRDS(fname_rds)\n",
    "head(df_p2g_epi)\n",
    "dim(df_p2g_epi)\n",
    "\n",
    "upeaks_epi <- unique(df_p2g_epi$peakName)\n",
    "n_upeaks_epi <- length(upeaks_epi)\n",
    "\n",
    "ugenes_epi <- unique(df_p2g_epi$geneName)\n",
    "n_ugenes_epi <- length(ugenes_epi)\n",
    "\n",
    "cat(sprintf(\"# unique peaks epi: %d\\n\", n_upeaks_epi))\n",
    "cat(sprintf(\"# unique genes epi: %d\\n\", n_ugenes_epi))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5ff8f9b2",
   "metadata": {},
   "source": [
    "## df_p2g_cse"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "2ed00d1b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A data.frame: 6 × 13</caption>\n",
       "<thead>\n",
       "\t<tr><th></th><th scope=col>idxATAC</th><th scope=col>idxRNA</th><th scope=col>Correlation</th><th scope=col>FDR</th><th scope=col>VarQATAC</th><th scope=col>VarQRNA</th><th scope=col>EmpPval</th><th scope=col>EmpFDR</th><th scope=col>geneName</th><th scope=col>peakName</th><th scope=col>peakType</th><th scope=col>idx</th><th scope=col>kmeans</th></tr>\n",
       "\t<tr><th></th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>1</th><td>29</td><td>3</td><td>0.5394961</td><td> 6.024423e-38</td><td>0.9396097</td><td>0.4338114</td><td>0.11278982</td><td>0.7965846</td><td>FAM41C </td><td>chr1:1079324-1079824</td><td>Distal</td><td>29-3</td><td>5</td></tr>\n",
       "\t<tr><th scope=row>2</th><td>24</td><td>7</td><td>0.7894052</td><td>5.401495e-105</td><td>0.7539227</td><td>0.5385226</td><td>0.01994288</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1068557-1069057</td><td>Distal</td><td>24-7</td><td>5</td></tr>\n",
       "\t<tr><th scope=row>3</th><td>25</td><td>7</td><td>0.7349978</td><td> 6.699672e-84</td><td>0.7787057</td><td>0.5385226</td><td>0.03031435</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1069078-1069578</td><td>Distal</td><td>25-7</td><td>2</td></tr>\n",
       "\t<tr><th scope=row>4</th><td>26</td><td>7</td><td>0.8462787</td><td>5.132060e-135</td><td>0.7508486</td><td>0.5385226</td><td>0.01255312</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1069752-1070252</td><td>Distal</td><td>26-7</td><td>2</td></tr>\n",
       "\t<tr><th scope=row>5</th><td>29</td><td>7</td><td>0.8539726</td><td>5.278697e-140</td><td>0.9396097</td><td>0.5385226</td><td>0.01176771</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1079324-1079824</td><td>Distal</td><td>29-7</td><td>5</td></tr>\n",
       "\t<tr><th scope=row>6</th><td>30</td><td>7</td><td>0.6868139</td><td> 3.617362e-69</td><td>0.4759030</td><td>0.5385226</td><td>0.04307672</td><td>0.7892789</td><td>PLEKHN1</td><td>chr1:1080052-1080552</td><td>Distal</td><td>30-7</td><td>5</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.frame: 6 × 13\n",
       "\\begin{tabular}{r|lllllllllllll}\n",
       "  & idxATAC & idxRNA & Correlation & FDR & VarQATAC & VarQRNA & EmpPval & EmpFDR & geneName & peakName & peakType & idx & kmeans\\\\\n",
       "  & <int> & <int> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <chr> & <chr> & <chr> & <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t1 & 29 & 3 & 0.5394961 &  6.024423e-38 & 0.9396097 & 0.4338114 & 0.11278982 & 0.7965846 & FAM41C  & chr1:1079324-1079824 & Distal & 29-3 & 5\\\\\n",
       "\t2 & 24 & 7 & 0.7894052 & 5.401495e-105 & 0.7539227 & 0.5385226 & 0.01994288 & 0.7892789 & PLEKHN1 & chr1:1068557-1069057 & Distal & 24-7 & 5\\\\\n",
       "\t3 & 25 & 7 & 0.7349978 &  6.699672e-84 & 0.7787057 & 0.5385226 & 0.03031435 & 0.7892789 & PLEKHN1 & chr1:1069078-1069578 & Distal & 25-7 & 2\\\\\n",
       "\t4 & 26 & 7 & 0.8462787 & 5.132060e-135 & 0.7508486 & 0.5385226 & 0.01255312 & 0.7892789 & PLEKHN1 & chr1:1069752-1070252 & Distal & 26-7 & 2\\\\\n",
       "\t5 & 29 & 7 & 0.8539726 & 5.278697e-140 & 0.9396097 & 0.5385226 & 0.01176771 & 0.7892789 & PLEKHN1 & chr1:1079324-1079824 & Distal & 29-7 & 5\\\\\n",
       "\t6 & 30 & 7 & 0.6868139 &  3.617362e-69 & 0.4759030 & 0.5385226 & 0.04307672 & 0.7892789 & PLEKHN1 & chr1:1080052-1080552 & Distal & 30-7 & 5\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.frame: 6 × 13\n",
       "\n",
       "| <!--/--> | idxATAC &lt;int&gt; | idxRNA &lt;int&gt; | Correlation &lt;dbl&gt; | FDR &lt;dbl&gt; | VarQATAC &lt;dbl&gt; | VarQRNA &lt;dbl&gt; | EmpPval &lt;dbl&gt; | EmpFDR &lt;dbl&gt; | geneName &lt;chr&gt; | peakName &lt;chr&gt; | peakType &lt;chr&gt; | idx &lt;chr&gt; | kmeans &lt;int&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| 1 | 29 | 3 | 0.5394961 |  6.024423e-38 | 0.9396097 | 0.4338114 | 0.11278982 | 0.7965846 | FAM41C  | chr1:1079324-1079824 | Distal | 29-3 | 5 |\n",
       "| 2 | 24 | 7 | 0.7894052 | 5.401495e-105 | 0.7539227 | 0.5385226 | 0.01994288 | 0.7892789 | PLEKHN1 | chr1:1068557-1069057 | Distal | 24-7 | 5 |\n",
       "| 3 | 25 | 7 | 0.7349978 |  6.699672e-84 | 0.7787057 | 0.5385226 | 0.03031435 | 0.7892789 | PLEKHN1 | chr1:1069078-1069578 | Distal | 25-7 | 2 |\n",
       "| 4 | 26 | 7 | 0.8462787 | 5.132060e-135 | 0.7508486 | 0.5385226 | 0.01255312 | 0.7892789 | PLEKHN1 | chr1:1069752-1070252 | Distal | 26-7 | 2 |\n",
       "| 5 | 29 | 7 | 0.8539726 | 5.278697e-140 | 0.9396097 | 0.5385226 | 0.01176771 | 0.7892789 | PLEKHN1 | chr1:1079324-1079824 | Distal | 29-7 | 5 |\n",
       "| 6 | 30 | 7 | 0.6868139 |  3.617362e-69 | 0.4759030 | 0.5385226 | 0.04307672 | 0.7892789 | PLEKHN1 | chr1:1080052-1080552 | Distal | 30-7 | 5 |\n",
       "\n"
      ],
      "text/plain": [
       "  idxATAC idxRNA Correlation FDR           VarQATAC  VarQRNA   EmpPval   \n",
       "1 29      3      0.5394961    6.024423e-38 0.9396097 0.4338114 0.11278982\n",
       "2 24      7      0.7894052   5.401495e-105 0.7539227 0.5385226 0.01994288\n",
       "3 25      7      0.7349978    6.699672e-84 0.7787057 0.5385226 0.03031435\n",
       "4 26      7      0.8462787   5.132060e-135 0.7508486 0.5385226 0.01255312\n",
       "5 29      7      0.8539726   5.278697e-140 0.9396097 0.5385226 0.01176771\n",
       "6 30      7      0.6868139    3.617362e-69 0.4759030 0.5385226 0.04307672\n",
       "  EmpFDR    geneName peakName             peakType idx  kmeans\n",
       "1 0.7965846 FAM41C   chr1:1079324-1079824 Distal   29-3 5     \n",
       "2 0.7892789 PLEKHN1  chr1:1068557-1069057 Distal   24-7 5     \n",
       "3 0.7892789 PLEKHN1  chr1:1069078-1069578 Distal   25-7 2     \n",
       "4 0.7892789 PLEKHN1  chr1:1069752-1070252 Distal   26-7 2     \n",
       "5 0.7892789 PLEKHN1  chr1:1079324-1079824 Distal   29-7 5     \n",
       "6 0.7892789 PLEKHN1  chr1:1080052-1080552 Distal   30-7 5     "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>11551</li><li>13</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 11551\n",
       "\\item 13\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 11551\n",
       "2. 13\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 11551    13"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# unique peaks cse: 5141\n",
      "# unique genes cse: 3586\n"
     ]
    }
   ],
   "source": [
    "peaktype <- \"enhancer\"\n",
    "fname_rds <- sprintf(\"%s/rds/cancer_specific_%s_p2g_table.rds\", dir_output_p2g, peaktype)\n",
    "\n",
    "df_p2g_cse <- readRDS(fname_rds)\n",
    "head(df_p2g_cse)\n",
    "dim(df_p2g_cse)\n",
    "\n",
    "upeaks_cse <- unique(df_p2g_cse$peakName)\n",
    "n_upeaks_cse <- length(upeaks_cse)\n",
    "\n",
    "ugenes_cse <- unique(df_p2g_cse$geneName)\n",
    "n_ugenes_cse <- length(ugenes_cse)\n",
    "\n",
    "cat(sprintf(\"# unique peaks cse: %d\\n\", n_upeaks_cse))\n",
    "cat(sprintf(\"# unique genes cse: %d\\n\", n_ugenes_cse))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "651aadc8",
   "metadata": {},
   "source": [
    "## df_p2g_normal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "42680ef1",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "comparision of non-Epi. vs. CSE\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A data.frame: 6 × 13</caption>\n",
       "<thead>\n",
       "\t<tr><th></th><th scope=col>idxATAC</th><th scope=col>idxRNA</th><th scope=col>Correlation</th><th scope=col>FDR</th><th scope=col>VarQATAC</th><th scope=col>VarQRNA</th><th scope=col>EmpPval</th><th scope=col>EmpFDR</th><th scope=col>geneName</th><th scope=col>peakName</th><th scope=col>peakType</th><th scope=col>idx</th><th scope=col>kmeans</th></tr>\n",
       "\t<tr><th></th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>77</th><td> 22</td><td>17</td><td>0.6037769</td><td>1.453477e-49</td><td>0.6319305</td><td>0.4842678</td><td>0.07564391</td><td>0.7892789</td><td>TNFRSF4</td><td>chr1:1059422-1059922</td><td>Distal</td><td>22-17 </td><td>1</td></tr>\n",
       "\t<tr><th scope=row>121</th><td> 77</td><td>31</td><td>0.5395152</td><td>5.981577e-38</td><td>0.8178778</td><td>0.6743580</td><td>0.11277696</td><td>0.7965691</td><td>CCNL2  </td><td>chr1:1430153-1430653</td><td>Distal</td><td>77-31 </td><td>5</td></tr>\n",
       "\t<tr><th scope=row>124</th><td> 77</td><td>33</td><td>0.6222581</td><td>2.030050e-53</td><td>0.8178778</td><td>0.3854527</td><td>0.06704292</td><td>0.7892789</td><td>ANKRD65</td><td>chr1:1430153-1430653</td><td>Distal</td><td>77-33 </td><td>5</td></tr>\n",
       "\t<tr><th scope=row>125</th><td> 85</td><td>34</td><td>0.4932488</td><td>5.055257e-31</td><td>0.5334295</td><td>0.8695504</td><td>0.14746854</td><td>0.8112124</td><td>VWA1   </td><td>chr1:1504831-1505331</td><td>Distal</td><td>85-34 </td><td>5</td></tr>\n",
       "\t<tr><th scope=row>132</th><td>119</td><td>49</td><td>0.6714273</td><td>4.744437e-65</td><td>0.8276508</td><td>0.8432451</td><td>0.04800736</td><td>0.7892789</td><td>GNB1   </td><td>chr1:1906167-1906667</td><td>Distal</td><td>119-49</td><td>5</td></tr>\n",
       "\t<tr><th scope=row>133</th><td>120</td><td>49</td><td>0.6480846</td><td>2.930064e-59</td><td>0.8340593</td><td>0.8432451</td><td>0.05638730</td><td>0.7892789</td><td>GNB1   </td><td>chr1:1908914-1909414</td><td>Distal</td><td>120-49</td><td>5</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.frame: 6 × 13\n",
       "\\begin{tabular}{r|lllllllllllll}\n",
       "  & idxATAC & idxRNA & Correlation & FDR & VarQATAC & VarQRNA & EmpPval & EmpFDR & geneName & peakName & peakType & idx & kmeans\\\\\n",
       "  & <int> & <int> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <chr> & <chr> & <chr> & <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t77 &  22 & 17 & 0.6037769 & 1.453477e-49 & 0.6319305 & 0.4842678 & 0.07564391 & 0.7892789 & TNFRSF4 & chr1:1059422-1059922 & Distal & 22-17  & 1\\\\\n",
       "\t121 &  77 & 31 & 0.5395152 & 5.981577e-38 & 0.8178778 & 0.6743580 & 0.11277696 & 0.7965691 & CCNL2   & chr1:1430153-1430653 & Distal & 77-31  & 5\\\\\n",
       "\t124 &  77 & 33 & 0.6222581 & 2.030050e-53 & 0.8178778 & 0.3854527 & 0.06704292 & 0.7892789 & ANKRD65 & chr1:1430153-1430653 & Distal & 77-33  & 5\\\\\n",
       "\t125 &  85 & 34 & 0.4932488 & 5.055257e-31 & 0.5334295 & 0.8695504 & 0.14746854 & 0.8112124 & VWA1    & chr1:1504831-1505331 & Distal & 85-34  & 5\\\\\n",
       "\t132 & 119 & 49 & 0.6714273 & 4.744437e-65 & 0.8276508 & 0.8432451 & 0.04800736 & 0.7892789 & GNB1    & chr1:1906167-1906667 & Distal & 119-49 & 5\\\\\n",
       "\t133 & 120 & 49 & 0.6480846 & 2.930064e-59 & 0.8340593 & 0.8432451 & 0.05638730 & 0.7892789 & GNB1    & chr1:1908914-1909414 & Distal & 120-49 & 5\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.frame: 6 × 13\n",
       "\n",
       "| <!--/--> | idxATAC &lt;int&gt; | idxRNA &lt;int&gt; | Correlation &lt;dbl&gt; | FDR &lt;dbl&gt; | VarQATAC &lt;dbl&gt; | VarQRNA &lt;dbl&gt; | EmpPval &lt;dbl&gt; | EmpFDR &lt;dbl&gt; | geneName &lt;chr&gt; | peakName &lt;chr&gt; | peakType &lt;chr&gt; | idx &lt;chr&gt; | kmeans &lt;int&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| 77 |  22 | 17 | 0.6037769 | 1.453477e-49 | 0.6319305 | 0.4842678 | 0.07564391 | 0.7892789 | TNFRSF4 | chr1:1059422-1059922 | Distal | 22-17  | 1 |\n",
       "| 121 |  77 | 31 | 0.5395152 | 5.981577e-38 | 0.8178778 | 0.6743580 | 0.11277696 | 0.7965691 | CCNL2   | chr1:1430153-1430653 | Distal | 77-31  | 5 |\n",
       "| 124 |  77 | 33 | 0.6222581 | 2.030050e-53 | 0.8178778 | 0.3854527 | 0.06704292 | 0.7892789 | ANKRD65 | chr1:1430153-1430653 | Distal | 77-33  | 5 |\n",
       "| 125 |  85 | 34 | 0.4932488 | 5.055257e-31 | 0.5334295 | 0.8695504 | 0.14746854 | 0.8112124 | VWA1    | chr1:1504831-1505331 | Distal | 85-34  | 5 |\n",
       "| 132 | 119 | 49 | 0.6714273 | 4.744437e-65 | 0.8276508 | 0.8432451 | 0.04800736 | 0.7892789 | GNB1    | chr1:1906167-1906667 | Distal | 119-49 | 5 |\n",
       "| 133 | 120 | 49 | 0.6480846 | 2.930064e-59 | 0.8340593 | 0.8432451 | 0.05638730 | 0.7892789 | GNB1    | chr1:1908914-1909414 | Distal | 120-49 | 5 |\n",
       "\n"
      ],
      "text/plain": [
       "    idxATAC idxRNA Correlation FDR          VarQATAC  VarQRNA   EmpPval   \n",
       "77   22     17     0.6037769   1.453477e-49 0.6319305 0.4842678 0.07564391\n",
       "121  77     31     0.5395152   5.981577e-38 0.8178778 0.6743580 0.11277696\n",
       "124  77     33     0.6222581   2.030050e-53 0.8178778 0.3854527 0.06704292\n",
       "125  85     34     0.4932488   5.055257e-31 0.5334295 0.8695504 0.14746854\n",
       "132 119     49     0.6714273   4.744437e-65 0.8276508 0.8432451 0.04800736\n",
       "133 120     49     0.6480846   2.930064e-59 0.8340593 0.8432451 0.05638730\n",
       "    EmpFDR    geneName peakName             peakType idx    kmeans\n",
       "77  0.7892789 TNFRSF4  chr1:1059422-1059922 Distal   22-17  1     \n",
       "121 0.7965691 CCNL2    chr1:1430153-1430653 Distal   77-31  5     \n",
       "124 0.7892789 ANKRD65  chr1:1430153-1430653 Distal   77-33  5     \n",
       "125 0.8112124 VWA1     chr1:1504831-1505331 Distal   85-34  5     \n",
       "132 0.7892789 GNB1     chr1:1906167-1906667 Distal   119-49 5     \n",
       "133 0.7892789 GNB1     chr1:1908914-1909414 Distal   120-49 5     "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>7594</li><li>13</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 7594\n",
       "\\item 13\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 7594\n",
       "2. 13\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 7594   13"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# unique peaks for non-Epi.: 4929\n",
      "# unique genes for non-Epi.: 3551\n"
     ]
    }
   ],
   "source": [
    "   \n",
    "#comparision of non-epi vs. epi  \n",
    "group_ref <- \"non-Epi.\"\n",
    "group1 <- \"CSE\"\n",
    "\n",
    "# df_p2g_normal contain non-epithelial p2g\n",
    "f <- which(!df_p2g$peakName %in% df_p2g_epi$peakName)\n",
    "df_p2g_normal <- df_p2g[f,]\n",
    "\n",
    "cat(sprintf(\"comparision of %s vs. %s\\n\", group_ref, group1))\n",
    "\n",
    "\n",
    "head(df_p2g_normal)\n",
    "dim(df_p2g_normal)\n",
    "\n",
    "upeaks_normal <- unique(df_p2g_normal$peakName)\n",
    "n_upeaks_normal <- length(upeaks_normal)\n",
    "\n",
    "ugenes_normal <- unique(df_p2g_normal$geneName)\n",
    "n_ugenes_normal <- length(ugenes_normal)\n",
    "\n",
    "cat(sprintf(\"# unique peaks for %s: %d\\n\", group_ref, n_upeaks_normal))\n",
    "cat(sprintf(\"# unique genes for %s: %d\\n\", group_ref, n_ugenes_normal))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "a08dd2e9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "107"
      ],
      "text/latex": [
       "107"
      ],
      "text/markdown": [
       "107"
      ],
      "text/plain": [
       "[1] 107"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "ugenes_common <- intersect(ugenes_cse, ugenes_normal)\n",
    "length(ugenes_common)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "6084d001",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "3479"
      ],
      "text/latex": [
       "3479"
      ],
      "text/markdown": [
       "3479"
      ],
      "text/plain": [
       "[1] 3479"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "ugenes_cse_only <- setdiff(ugenes_cse, ugenes_normal)\n",
    "length(ugenes_cse_only)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "34728ca0",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "3444"
      ],
      "text/latex": [
       "3444"
      ],
      "text/markdown": [
       "3444"
      ],
      "text/plain": [
       "[1] 3444"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "ugenes_normal_only <- setdiff(ugenes_normal, ugenes_cse)\n",
    "length(ugenes_normal_only)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5b915017",
   "metadata": {},
   "source": [
    "## barplot"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dbe55c0e",
   "metadata": {},
   "source": [
    "### total # of genes linked with peaks"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "0545e3f8",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A data.frame: 2 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>type_normal_cancer</th><th scope=col>geneCount</th></tr>\n",
       "\t<tr><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>non-Epi.</td><td>3551</td></tr>\n",
       "\t<tr><td>CSE     </td><td>3586</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.frame: 2 × 2\n",
       "\\begin{tabular}{ll}\n",
       " type\\_normal\\_cancer & geneCount\\\\\n",
       " <fct> & <int>\\\\\n",
       "\\hline\n",
       "\t non-Epi. & 3551\\\\\n",
       "\t CSE      & 3586\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.frame: 2 × 2\n",
       "\n",
       "| type_normal_cancer &lt;fct&gt; | geneCount &lt;int&gt; |\n",
       "|---|---|\n",
       "| non-Epi. | 3551 |\n",
       "| CSE      | 3586 |\n",
       "\n"
      ],
      "text/plain": [
       "  type_normal_cancer geneCount\n",
       "1 non-Epi.           3551     \n",
       "2 CSE                3586     "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "image/png": 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K2WsPQinrHHio3jDfz8nnA7HACAPFIx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\nSUVORK5CYII=",
      "text/plain": [
       "plot without title"
      ]
     },
     "metadata": {
      "image/png": {
       "height": 240,
       "width": 198
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "\n",
    "df_g <- data.frame(type_normal_cancer=factor(c(group_ref, group1), levels=c(group_ref, group1)),\n",
    "            geneCount=c(\n",
    "                n_ugenes_normal,\n",
    "                n_ugenes_cse\n",
    "            ))\n",
    "\n",
    "df_g\n",
    "\n",
    "nv_colors_normal_cancer <- c(\"#93CEFF\", \"forestgreen\")\n",
    "names(nv_colors_normal_cancer) <- c(group_ref, group1)\n",
    "\n",
    "str_condition_plot <- sprintf(\"%s_%s-vs-%s_ngenes_linked%s\", str_condition, group_ref, group1, filename_appendix)\n",
    "\n",
    "gg <- print_ggpubr(df_g,\n",
    "            x = \"type_normal_cancer\", y = \"geneCount\",\n",
    "            color = \"type_normal_cancer\", \n",
    "            fill = \"type_normal_cancer\", \n",
    "            order_x = c(group_ref, group1),\n",
    "            facet.by = NULL, facet.ncol = 5,\n",
    "            plot_type = \"barplot\",\n",
    "            #list_comparison = list(c(\"Normal\", \"Cancer\")),\n",
    "            #symnum.args = NULL,\n",
    "            step.increase = 0.03, label.y = 1500, vjust = -0.4, tip.length = c(0.05, 0.05),\n",
    "            test = NULL, test_label.x = 1, test_label.y = 1, test_vjust = 0.5,\n",
    "            color_manual = nv_colors_normal_cancer,\n",
    "            fill_manual = nv_colors_normal_cancer,\n",
    "            ylimits = c(0, 4500),\n",
    "            ybreaks = pretty(c(0, 6000), n = 4),\n",
    "            yexpand = c(0, 0),\n",
    "            yintercept = NULL,\n",
    "            xlim = NULL, ylim = NULL,\n",
    "            xlab = \"\", ylab = \"total # of linked genes\",\n",
    "            angle = 0, font_size = 13,\n",
    "            theme_style = \"simple\",\n",
    "            width = 3.3, height = 4,\n",
    "            str_condition_plot = str_condition_plot,\n",
    "            n_log = 0)\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8e1836b0",
   "metadata": {},
   "source": [
    "###  num of genes per peak"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6eb6fb60",
   "metadata": {},
   "source": [
    "#### df_summary.normal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "b6b6a326",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>7594</li><li>13</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 7594\n",
       "\\item 13\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 7594\n",
       "2. 13\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 7594   13"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# peaks for non-Epi.: 7594\n",
      "# unique peaks for non-Epi.: 4929\n",
      "# unique genes for non-Epi.: 3551\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A grouped_df: 6 × 3</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>peakName</th><th scope=col>geneName</th><th scope=col>n</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>chr1:100292596-100293096</td><td>CDC14A</td><td>1</td></tr>\n",
       "\t<tr><td>chr1:100621997-100622497</td><td>VCAM1 </td><td>1</td></tr>\n",
       "\t<tr><td>chr1:101111990-101112490</td><td>S1PR1 </td><td>1</td></tr>\n",
       "\t<tr><td>chr1:101161496-101161996</td><td>S1PR1 </td><td>1</td></tr>\n",
       "\t<tr><td>chr1:101181920-101182420</td><td>S1PR1 </td><td>1</td></tr>\n",
       "\t<tr><td>chr1:101242272-101242772</td><td>S1PR1 </td><td>1</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A grouped\\_df: 6 × 3\n",
       "\\begin{tabular}{lll}\n",
       " peakName & geneName & n\\\\\n",
       " <chr> & <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t chr1:100292596-100293096 & CDC14A & 1\\\\\n",
       "\t chr1:100621997-100622497 & VCAM1  & 1\\\\\n",
       "\t chr1:101111990-101112490 & S1PR1  & 1\\\\\n",
       "\t chr1:101161496-101161996 & S1PR1  & 1\\\\\n",
       "\t chr1:101181920-101182420 & S1PR1  & 1\\\\\n",
       "\t chr1:101242272-101242772 & S1PR1  & 1\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A grouped_df: 6 × 3\n",
       "\n",
       "| peakName &lt;chr&gt; | geneName &lt;chr&gt; | n &lt;int&gt; |\n",
       "|---|---|---|\n",
       "| chr1:100292596-100293096 | CDC14A | 1 |\n",
       "| chr1:100621997-100622497 | VCAM1  | 1 |\n",
       "| chr1:101111990-101112490 | S1PR1  | 1 |\n",
       "| chr1:101161496-101161996 | S1PR1  | 1 |\n",
       "| chr1:101181920-101182420 | S1PR1  | 1 |\n",
       "| chr1:101242272-101242772 | S1PR1  | 1 |\n",
       "\n"
      ],
      "text/plain": [
       "  peakName                 geneName n\n",
       "1 chr1:100292596-100293096 CDC14A   1\n",
       "2 chr1:100621997-100622497 VCAM1    1\n",
       "3 chr1:101111990-101112490 S1PR1    1\n",
       "4 chr1:101161496-101161996 S1PR1    1\n",
       "5 chr1:101181920-101182420 S1PR1    1\n",
       "6 chr1:101242272-101242772 S1PR1    1"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>7594</li><li>3</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 7594\n",
       "\\item 3\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 7594\n",
       "2. 3\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 7594    3"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A tibble: 6 × 3</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>peakName</th><th scope=col>genes</th><th scope=col>n</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>chr6:30500589-30501089  </td><td>ABCF1, ATAT1, C6orf136, DHX16, GNL1, HLA-E, MDC1, PPP1R18, TRIM39          </td><td>9</td></tr>\n",
       "\t<tr><td>chr11:64331686-64332186 </td><td>CCDC88B, DNAJC4, FERMT3, NUDT22, PLCB3, PRDX5, TRMT112, TRPT1              </td><td>8</td></tr>\n",
       "\t<tr><td>chr6:32794409-32794909  </td><td>HLA-DMA, HLA-DMB, HLA-DOA, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1</td><td>8</td></tr>\n",
       "\t<tr><td>chr9:136642306-136642806</td><td>CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                 </td><td>8</td></tr>\n",
       "\t<tr><td>chr9:136644791-136645291</td><td>CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                 </td><td>8</td></tr>\n",
       "\t<tr><td>chr9:136646343-136646843</td><td>CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                 </td><td>8</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A tibble: 6 × 3\n",
       "\\begin{tabular}{lll}\n",
       " peakName & genes & n\\\\\n",
       " <chr> & <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t chr6:30500589-30501089   & ABCF1, ATAT1, C6orf136, DHX16, GNL1, HLA-E, MDC1, PPP1R18, TRIM39           & 9\\\\\n",
       "\t chr11:64331686-64332186  & CCDC88B, DNAJC4, FERMT3, NUDT22, PLCB3, PRDX5, TRMT112, TRPT1               & 8\\\\\n",
       "\t chr6:32794409-32794909   & HLA-DMA, HLA-DMB, HLA-DOA, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1 & 8\\\\\n",
       "\t chr9:136642306-136642806 & CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                  & 8\\\\\n",
       "\t chr9:136644791-136645291 & CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                  & 8\\\\\n",
       "\t chr9:136646343-136646843 & CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                  & 8\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A tibble: 6 × 3\n",
       "\n",
       "| peakName &lt;chr&gt; | genes &lt;chr&gt; | n &lt;int&gt; |\n",
       "|---|---|---|\n",
       "| chr6:30500589-30501089   | ABCF1, ATAT1, C6orf136, DHX16, GNL1, HLA-E, MDC1, PPP1R18, TRIM39           | 9 |\n",
       "| chr11:64331686-64332186  | CCDC88B, DNAJC4, FERMT3, NUDT22, PLCB3, PRDX5, TRMT112, TRPT1               | 8 |\n",
       "| chr6:32794409-32794909   | HLA-DMA, HLA-DMB, HLA-DOA, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1 | 8 |\n",
       "| chr9:136642306-136642806 | CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                  | 8 |\n",
       "| chr9:136644791-136645291 | CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                  | 8 |\n",
       "| chr9:136646343-136646843 | CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                  | 8 |\n",
       "\n"
      ],
      "text/plain": [
       "  peakName                \n",
       "1 chr6:30500589-30501089  \n",
       "2 chr11:64331686-64332186 \n",
       "3 chr6:32794409-32794909  \n",
       "4 chr9:136642306-136642806\n",
       "5 chr9:136644791-136645291\n",
       "6 chr9:136646343-136646843\n",
       "  genes                                                                       n\n",
       "1 ABCF1, ATAT1, C6orf136, DHX16, GNL1, HLA-E, MDC1, PPP1R18, TRIM39           9\n",
       "2 CCDC88B, DNAJC4, FERMT3, NUDT22, PLCB3, PRDX5, TRMT112, TRPT1               8\n",
       "3 HLA-DMA, HLA-DMB, HLA-DOA, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRB1 8\n",
       "4 CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                  8\n",
       "5 CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                  8\n",
       "6 CCDC183, EGFL7, INPP5E, LCN6, NOTCH1, RABL6, SEC16A, TRAF2                  8"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A tibble: 6 × 3</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>peakName</th><th scope=col>genes</th><th scope=col>n</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>chrX:48487219-48487719</td><td>SLC38A5</td><td>1</td></tr>\n",
       "\t<tr><td>chrX:50838826-50839326</td><td>SHROOM4</td><td>1</td></tr>\n",
       "\t<tr><td>chrX:68894918-68895418</td><td>STARD8 </td><td>1</td></tr>\n",
       "\t<tr><td>chrX:71871303-71871803</td><td>NHSL2  </td><td>1</td></tr>\n",
       "\t<tr><td>chrX:96436073-96436573</td><td>DIAPH2 </td><td>1</td></tr>\n",
       "\t<tr><td>chrX:96564612-96565112</td><td>DIAPH2 </td><td>1</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A tibble: 6 × 3\n",
       "\\begin{tabular}{lll}\n",
       " peakName & genes & n\\\\\n",
       " <chr> & <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t chrX:48487219-48487719 & SLC38A5 & 1\\\\\n",
       "\t chrX:50838826-50839326 & SHROOM4 & 1\\\\\n",
       "\t chrX:68894918-68895418 & STARD8  & 1\\\\\n",
       "\t chrX:71871303-71871803 & NHSL2   & 1\\\\\n",
       "\t chrX:96436073-96436573 & DIAPH2  & 1\\\\\n",
       "\t chrX:96564612-96565112 & DIAPH2  & 1\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A tibble: 6 × 3\n",
       "\n",
       "| peakName &lt;chr&gt; | genes &lt;chr&gt; | n &lt;int&gt; |\n",
       "|---|---|---|\n",
       "| chrX:48487219-48487719 | SLC38A5 | 1 |\n",
       "| chrX:50838826-50839326 | SHROOM4 | 1 |\n",
       "| chrX:68894918-68895418 | STARD8  | 1 |\n",
       "| chrX:71871303-71871803 | NHSL2   | 1 |\n",
       "| chrX:96436073-96436573 | DIAPH2  | 1 |\n",
       "| chrX:96564612-96565112 | DIAPH2  | 1 |\n",
       "\n"
      ],
      "text/plain": [
       "  peakName               genes   n\n",
       "1 chrX:48487219-48487719 SLC38A5 1\n",
       "2 chrX:50838826-50839326 SHROOM4 1\n",
       "3 chrX:68894918-68895418 STARD8  1\n",
       "4 chrX:71871303-71871803 NHSL2   1\n",
       "5 chrX:96436073-96436573 DIAPH2  1\n",
       "6 chrX:96564612-96565112 DIAPH2  1"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>4929</li><li>3</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 4929\n",
       "\\item 3\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 4929\n",
       "2. 3\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 4929    3"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "7594"
      ],
      "text/latex": [
       "7594"
      ],
      "text/markdown": [
       "7594"
      ],
      "text/plain": [
       "[1] 7594"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "1.54067762223575"
      ],
      "text/latex": [
       "1.54067762223575"
      ],
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       "1.54067762223575"
      ],
      "text/plain": [
       "[1] 1.540678"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "dim(df_p2g_normal)\n",
    "\n",
    "n_peaks_normal <- dim(df_p2g_normal)[1]\n",
    "cat(sprintf(\"# peaks for %s: %d\\n\", group_ref, n_peaks_normal))\n",
    "\n",
    "n_upeaks_normal <- length(unique(df_p2g_normal$peakName))\n",
    "n_ugenes_normal <- length(unique(df_p2g_normal$geneName))\n",
    "cat(sprintf(\"# unique peaks for %s: %d\\n\", group_ref, n_upeaks_normal))\n",
    "cat(sprintf(\"# unique genes for %s: %d\\n\", group_ref, n_ugenes_normal))\n",
    "\n",
    "df_summary <- df_p2g_normal %>% group_by(peakName) %>% dplyr::count(geneName)\n",
    "df_summary <- df_summary[order(df_summary$n, decreasing=T),]\n",
    "head(df_summary)\n",
    "dim(df_summary)\n",
    "\n",
    "df_summary <- df_p2g_normal %>% group_by(peakName) %>% \n",
    "                    dplyr::summarise(genes=paste(sort(unique(geneName)), collapse=\", \"),\n",
    "                                     n = n_distinct(geneName))\n",
    "df_summary.normal <- df_summary[order(df_summary$n, decreasing=T),]\n",
    "head(df_summary.normal)\n",
    "tail(df_summary.normal)\n",
    "dim(df_summary.normal)\n",
    "sum(df_summary.normal$n)\n",
    "mean(df_summary.normal$n)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4fba6a58",
   "metadata": {},
   "source": [
    "#### df_summary.cse"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "f536ef2a",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>11551</li><li>13</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 11551\n",
       "\\item 13\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 11551\n",
       "2. 13\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 11551    13"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# peaks for CSE: 11551\n",
      "# unique peaks for CSE: 5141\n",
      "# unique genes for CSE: 3586\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A grouped_df: 6 × 3</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>peakName</th><th scope=col>geneName</th><th scope=col>n</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>chr1:10018448-10018948</td><td>CLSTN1  </td><td>1</td></tr>\n",
       "\t<tr><td>chr1:10018448-10018948</td><td>CTNNBIP1</td><td>1</td></tr>\n",
       "\t<tr><td>chr1:10018448-10018948</td><td>LZIC    </td><td>1</td></tr>\n",
       "\t<tr><td>chr1:10018448-10018948</td><td>NMNAT1  </td><td>1</td></tr>\n",
       "\t<tr><td>chr1:1068557-1069057  </td><td>ACAP3   </td><td>1</td></tr>\n",
       "\t<tr><td>chr1:1068557-1069057  </td><td>AGRN    </td><td>1</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A grouped\\_df: 6 × 3\n",
       "\\begin{tabular}{lll}\n",
       " peakName & geneName & n\\\\\n",
       " <chr> & <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t chr1:10018448-10018948 & CLSTN1   & 1\\\\\n",
       "\t chr1:10018448-10018948 & CTNNBIP1 & 1\\\\\n",
       "\t chr1:10018448-10018948 & LZIC     & 1\\\\\n",
       "\t chr1:10018448-10018948 & NMNAT1   & 1\\\\\n",
       "\t chr1:1068557-1069057   & ACAP3    & 1\\\\\n",
       "\t chr1:1068557-1069057   & AGRN     & 1\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A grouped_df: 6 × 3\n",
       "\n",
       "| peakName &lt;chr&gt; | geneName &lt;chr&gt; | n &lt;int&gt; |\n",
       "|---|---|---|\n",
       "| chr1:10018448-10018948 | CLSTN1   | 1 |\n",
       "| chr1:10018448-10018948 | CTNNBIP1 | 1 |\n",
       "| chr1:10018448-10018948 | LZIC     | 1 |\n",
       "| chr1:10018448-10018948 | NMNAT1   | 1 |\n",
       "| chr1:1068557-1069057   | ACAP3    | 1 |\n",
       "| chr1:1068557-1069057   | AGRN     | 1 |\n",
       "\n"
      ],
      "text/plain": [
       "  peakName               geneName n\n",
       "1 chr1:10018448-10018948 CLSTN1   1\n",
       "2 chr1:10018448-10018948 CTNNBIP1 1\n",
       "3 chr1:10018448-10018948 LZIC     1\n",
       "4 chr1:10018448-10018948 NMNAT1   1\n",
       "5 chr1:1068557-1069057   ACAP3    1\n",
       "6 chr1:1068557-1069057   AGRN     1"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>11551</li><li>3</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 11551\n",
       "\\item 3\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 11551\n",
       "2. 3\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 11551     3"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A tibble: 6 × 3</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>peakName</th><th scope=col>genes</th><th scope=col>n</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>chr1:155124589-155125089</td><td>ADAM15, CLK2, DCST1-AS1, DCST2, DPM3, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, HCN3, KRTCAP2, MTX1, MUC1, PMVK, PYGO2, RUSC1, RUSC1-AS1, SCAMP3, SLC50A1, ZBTB7B</td><td>21</td></tr>\n",
       "\t<tr><td>chr16:1900082-1900582   </td><td>EME2, FAHD1, GFER, HAGH, JPT2, MEIOB, MRPS34, MSRB1, NDUFB10, NME3, NOXO1, NPW, NTHL1, NUBP2, PKD1, RPS2, SNHG9, SYNGR3, TBL3, TSC2, ZNF598                 </td><td>21</td></tr>\n",
       "\t<tr><td>chr1:155117581-155118081</td><td>ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, HCN3, KRTCAP2, MTX1, MUC1, PMVK, PYGO2, RUSC1, RUSC1-AS1, SCAMP3, SLC50A1, ZBTB7B      </td><td>20</td></tr>\n",
       "\t<tr><td>chr16:1935255-1935755   </td><td>EME2, FAHD1, GFER, HAGH, MRPS34, MSRB1, NDUFB10, NME3, NOXO1, NTHL1, NUBP2, PKD1, RPS2, SNHG19, SNHG9, SYNGR3, TBL3, TRAF7, TSC2, ZNF598                    </td><td>20</td></tr>\n",
       "\t<tr><td>chr1:155222900-155223400</td><td>ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, GBA, HCN3, KRTCAP2, LENEP, MTX1, MUC1, RUSC1, SCAMP3, SLC50A1, ZBTB7B                  </td><td>19</td></tr>\n",
       "\t<tr><td>chr1:155224624-155225124</td><td>ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, GBA, HCN3, KRTCAP2, MTX1, MUC1, RUSC1, SCAMP3, SLC50A1, ZBTB7B                         </td><td>18</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A tibble: 6 × 3\n",
       "\\begin{tabular}{lll}\n",
       " peakName & genes & n\\\\\n",
       " <chr> & <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t chr1:155124589-155125089 & ADAM15, CLK2, DCST1-AS1, DCST2, DPM3, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, HCN3, KRTCAP2, MTX1, MUC1, PMVK, PYGO2, RUSC1, RUSC1-AS1, SCAMP3, SLC50A1, ZBTB7B & 21\\\\\n",
       "\t chr16:1900082-1900582    & EME2, FAHD1, GFER, HAGH, JPT2, MEIOB, MRPS34, MSRB1, NDUFB10, NME3, NOXO1, NPW, NTHL1, NUBP2, PKD1, RPS2, SNHG9, SYNGR3, TBL3, TSC2, ZNF598                  & 21\\\\\n",
       "\t chr1:155117581-155118081 & ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, HCN3, KRTCAP2, MTX1, MUC1, PMVK, PYGO2, RUSC1, RUSC1-AS1, SCAMP3, SLC50A1, ZBTB7B       & 20\\\\\n",
       "\t chr16:1935255-1935755    & EME2, FAHD1, GFER, HAGH, MRPS34, MSRB1, NDUFB10, NME3, NOXO1, NTHL1, NUBP2, PKD1, RPS2, SNHG19, SNHG9, SYNGR3, TBL3, TRAF7, TSC2, ZNF598                     & 20\\\\\n",
       "\t chr1:155222900-155223400 & ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, GBA, HCN3, KRTCAP2, LENEP, MTX1, MUC1, RUSC1, SCAMP3, SLC50A1, ZBTB7B                   & 19\\\\\n",
       "\t chr1:155224624-155225124 & ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, GBA, HCN3, KRTCAP2, MTX1, MUC1, RUSC1, SCAMP3, SLC50A1, ZBTB7B                          & 18\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A tibble: 6 × 3\n",
       "\n",
       "| peakName &lt;chr&gt; | genes &lt;chr&gt; | n &lt;int&gt; |\n",
       "|---|---|---|\n",
       "| chr1:155124589-155125089 | ADAM15, CLK2, DCST1-AS1, DCST2, DPM3, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, HCN3, KRTCAP2, MTX1, MUC1, PMVK, PYGO2, RUSC1, RUSC1-AS1, SCAMP3, SLC50A1, ZBTB7B | 21 |\n",
       "| chr16:1900082-1900582    | EME2, FAHD1, GFER, HAGH, JPT2, MEIOB, MRPS34, MSRB1, NDUFB10, NME3, NOXO1, NPW, NTHL1, NUBP2, PKD1, RPS2, SNHG9, SYNGR3, TBL3, TSC2, ZNF598                  | 21 |\n",
       "| chr1:155117581-155118081 | ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, HCN3, KRTCAP2, MTX1, MUC1, PMVK, PYGO2, RUSC1, RUSC1-AS1, SCAMP3, SLC50A1, ZBTB7B       | 20 |\n",
       "| chr16:1935255-1935755    | EME2, FAHD1, GFER, HAGH, MRPS34, MSRB1, NDUFB10, NME3, NOXO1, NTHL1, NUBP2, PKD1, RPS2, SNHG19, SNHG9, SYNGR3, TBL3, TRAF7, TSC2, ZNF598                     | 20 |\n",
       "| chr1:155222900-155223400 | ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, GBA, HCN3, KRTCAP2, LENEP, MTX1, MUC1, RUSC1, SCAMP3, SLC50A1, ZBTB7B                   | 19 |\n",
       "| chr1:155224624-155225124 | ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, GBA, HCN3, KRTCAP2, MTX1, MUC1, RUSC1, SCAMP3, SLC50A1, ZBTB7B                          | 18 |\n",
       "\n"
      ],
      "text/plain": [
       "  peakName                \n",
       "1 chr1:155124589-155125089\n",
       "2 chr16:1900082-1900582   \n",
       "3 chr1:155117581-155118081\n",
       "4 chr16:1935255-1935755   \n",
       "5 chr1:155222900-155223400\n",
       "6 chr1:155224624-155225124\n",
       "  genes                                                                                                                                                       \n",
       "1 ADAM15, CLK2, DCST1-AS1, DCST2, DPM3, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, HCN3, KRTCAP2, MTX1, MUC1, PMVK, PYGO2, RUSC1, RUSC1-AS1, SCAMP3, SLC50A1, ZBTB7B\n",
       "2 EME2, FAHD1, GFER, HAGH, JPT2, MEIOB, MRPS34, MSRB1, NDUFB10, NME3, NOXO1, NPW, NTHL1, NUBP2, PKD1, RPS2, SNHG9, SYNGR3, TBL3, TSC2, ZNF598                 \n",
       "3 ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, HCN3, KRTCAP2, MTX1, MUC1, PMVK, PYGO2, RUSC1, RUSC1-AS1, SCAMP3, SLC50A1, ZBTB7B      \n",
       "4 EME2, FAHD1, GFER, HAGH, MRPS34, MSRB1, NDUFB10, NME3, NOXO1, NTHL1, NUBP2, PKD1, RPS2, SNHG19, SNHG9, SYNGR3, TBL3, TRAF7, TSC2, ZNF598                    \n",
       "5 ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, GBA, HCN3, KRTCAP2, LENEP, MTX1, MUC1, RUSC1, SCAMP3, SLC50A1, ZBTB7B                  \n",
       "6 ADAM15, CLK2, DCST1-AS1, DCST2, EFNA1, EFNA3, EFNA4, FAM189B, FLAD1, GBA, HCN3, KRTCAP2, MTX1, MUC1, RUSC1, SCAMP3, SLC50A1, ZBTB7B                         \n",
       "  n \n",
       "1 21\n",
       "2 21\n",
       "3 20\n",
       "4 20\n",
       "5 19\n",
       "6 18"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A tibble: 6 × 3</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>peakName</th><th scope=col>genes</th><th scope=col>n</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>chrX:56920258-56920758</td><td>SPIN3  </td><td>1</td></tr>\n",
       "\t<tr><td>chrX:56946147-56946647</td><td>SPIN3  </td><td>1</td></tr>\n",
       "\t<tr><td>chrX:57643615-57644115</td><td>NLRP2B </td><td>1</td></tr>\n",
       "\t<tr><td>chrX:68489963-68490463</td><td>YIPF6  </td><td>1</td></tr>\n",
       "\t<tr><td>chrX:74382625-74383125</td><td>SLC16A2</td><td>1</td></tr>\n",
       "\t<tr><td>chrX:8067709-8068209  </td><td>PNPLA4 </td><td>1</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A tibble: 6 × 3\n",
       "\\begin{tabular}{lll}\n",
       " peakName & genes & n\\\\\n",
       " <chr> & <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t chrX:56920258-56920758 & SPIN3   & 1\\\\\n",
       "\t chrX:56946147-56946647 & SPIN3   & 1\\\\\n",
       "\t chrX:57643615-57644115 & NLRP2B  & 1\\\\\n",
       "\t chrX:68489963-68490463 & YIPF6   & 1\\\\\n",
       "\t chrX:74382625-74383125 & SLC16A2 & 1\\\\\n",
       "\t chrX:8067709-8068209   & PNPLA4  & 1\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A tibble: 6 × 3\n",
       "\n",
       "| peakName &lt;chr&gt; | genes &lt;chr&gt; | n &lt;int&gt; |\n",
       "|---|---|---|\n",
       "| chrX:56920258-56920758 | SPIN3   | 1 |\n",
       "| chrX:56946147-56946647 | SPIN3   | 1 |\n",
       "| chrX:57643615-57644115 | NLRP2B  | 1 |\n",
       "| chrX:68489963-68490463 | YIPF6   | 1 |\n",
       "| chrX:74382625-74383125 | SLC16A2 | 1 |\n",
       "| chrX:8067709-8068209   | PNPLA4  | 1 |\n",
       "\n"
      ],
      "text/plain": [
       "  peakName               genes   n\n",
       "1 chrX:56920258-56920758 SPIN3   1\n",
       "2 chrX:56946147-56946647 SPIN3   1\n",
       "3 chrX:57643615-57644115 NLRP2B  1\n",
       "4 chrX:68489963-68490463 YIPF6   1\n",
       "5 chrX:74382625-74383125 SLC16A2 1\n",
       "6 chrX:8067709-8068209   PNPLA4  1"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>5141</li><li>3</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 5141\n",
       "\\item 3\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 5141\n",
       "2. 3\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 5141    3"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "11551"
      ],
      "text/latex": [
       "11551"
      ],
      "text/markdown": [
       "11551"
      ],
      "text/plain": [
       "[1] 11551"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "2.24683913635479"
      ],
      "text/latex": [
       "2.24683913635479"
      ],
      "text/markdown": [
       "2.24683913635479"
      ],
      "text/plain": [
       "[1] 2.246839"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "dim(df_p2g_cse)\n",
    "\n",
    "n_peaks_cse <- dim(df_p2g_cse)[1]\n",
    "cat(sprintf(\"# peaks for %s: %d\\n\", group1, n_peaks_cse))\n",
    "\n",
    "n_upeaks_cse <- length(unique(df_p2g_cse$peakName))\n",
    "n_ugenes_cse <- length(unique(df_p2g_cse$geneName))\n",
    "cat(sprintf(\"# unique peaks for %s: %d\\n\", group1, n_upeaks_cse))\n",
    "cat(sprintf(\"# unique genes for %s: %d\\n\", group1, n_ugenes_cse))\n",
    "\n",
    "df_summary <- df_p2g_cse %>% group_by(peakName) %>% dplyr::count(geneName)\n",
    "df_summary <- df_summary[order(df_summary$n, decreasing=T),]\n",
    "head(df_summary)\n",
    "dim(df_summary)\n",
    "\n",
    "df_summary <- df_p2g_cse %>% group_by(peakName) %>% \n",
    "                    dplyr::summarise(genes=paste(sort(unique(geneName)), collapse=\", \"),\n",
    "                                     n = n_distinct(geneName))\n",
    "df_summary.cse <- df_summary[order(df_summary$n, decreasing=T),]\n",
    "head(df_summary.cse)\n",
    "tail(df_summary.cse)\n",
    "dim(df_summary.cse)\n",
    "sum(df_summary.cse$n)\n",
    "mean(df_summary.cse$n)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6a3d7181",
   "metadata": {},
   "source": [
    "#### print"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "d5dd1cef",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A data.frame: 2 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>type_normal_cancer</th><th scope=col>geneCount</th></tr>\n",
       "\t<tr><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;dbl&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>non-Epi.</td><td>1.540678</td></tr>\n",
       "\t<tr><td>CSE     </td><td>2.246839</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.frame: 2 × 2\n",
       "\\begin{tabular}{ll}\n",
       " type\\_normal\\_cancer & geneCount\\\\\n",
       " <fct> & <dbl>\\\\\n",
       "\\hline\n",
       "\t non-Epi. & 1.540678\\\\\n",
       "\t CSE      & 2.246839\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.frame: 2 × 2\n",
       "\n",
       "| type_normal_cancer &lt;fct&gt; | geneCount &lt;dbl&gt; |\n",
       "|---|---|\n",
       "| non-Epi. | 1.540678 |\n",
       "| CSE      | 2.246839 |\n",
       "\n"
      ],
      "text/plain": [
       "  type_normal_cancer geneCount\n",
       "1 non-Epi.           1.540678 \n",
       "2 CSE                2.246839 "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "image/png": 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3nE9OOIDgAgEgmOlLO7ziiMPPHmjVtn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",
      "text/plain": [
       "plot without title"
      ]
     },
     "metadata": {
      "image/png": {
       "height": 240,
       "width": 180
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "\n",
    "df_g <- data.frame(type_normal_cancer=factor(c(group_ref, group1), levels=c(group_ref, group1)),\n",
    "            geneCount=c(\n",
    "                mean(df_summary.normal$n),\n",
    "                mean(df_summary.cse$n)\n",
    "            ))\n",
    "\n",
    "df_g\n",
    "\n",
    "str_condition_plot <- sprintf(\"%s_%s-vs-%s_ngenes_linked_per_peak%s\", str_condition,\n",
    "                              group_ref, group1, filename_appendix)\n",
    "\n",
    "gg <- print_ggpubr(df_g,\n",
    "            x = \"type_normal_cancer\", y = \"geneCount\",\n",
    "            color = \"type_normal_cancer\", \n",
    "            fill = \"type_normal_cancer\", \n",
    "            order_x = c(group_ref, group1),\n",
    "            facet.by = NULL, facet.ncol = 5,\n",
    "            plot_type = \"barplot\",\n",
    "            #list_comparison = list(c(\"Normal\", \"Cancer\")),\n",
    "            #symnum.args = NULL,\n",
    "            step.increase = 0.03, label.y = 2.75, vjust = -0.4, tip.length = c(0.05, 0.05),\n",
    "            test = NULL, test_label.x = 1, test_label.y = 1, test_vjust = 0.5,\n",
    "            color_manual = nv_colors_normal_cancer,\n",
    "            fill_manual = nv_colors_normal_cancer,\n",
    "            ylimits = c(0, 2.5),\n",
    "            ybreaks = pretty(c(0, 2.5), n = 3),\n",
    "            yexpand = c(0, 0),\n",
    "            yintercept = NULL,\n",
    "            xlim = NULL, ylim = NULL,\n",
    "            xlab = \"\", ylab = \"# of linked genes per peak\",\n",
    "            angle = 0, font_size = 13,\n",
    "            theme_style = \"simple\",\n",
    "            width = 3, height = 4,\n",
    "            str_condition_plot = str_condition_plot,\n",
    "            n_log = 0)\n"
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