{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# R Graphics Exercise\n",
    "\n",
    "Do exercises 1-4 and if you have lots of time, exercise 5. In each case, your aim is to create a figure similar to the one shown for the pilot data set."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Registered S3 methods overwritten by 'ggplot2':\n",
      "  method         from \n",
      "  [.quosures     rlang\n",
      "  c.quosures     rlang\n",
      "  print.quosures rlang\n",
      "── \u001b[1mAttaching packages\u001b[22m ─────────────────────────────────────── tidyverse 1.2.1 ──\n",
      "\u001b[32m✔\u001b[39m \u001b[34mggplot2\u001b[39m 3.1.1     \u001b[32m✔\u001b[39m \u001b[34mpurrr  \u001b[39m 0.3.2\n",
      "\u001b[32m✔\u001b[39m \u001b[34mtibble \u001b[39m 2.1.2     \u001b[32m✔\u001b[39m \u001b[34mdplyr  \u001b[39m 0.8.1\n",
      "\u001b[32m✔\u001b[39m \u001b[34mtidyr  \u001b[39m 0.8.3     \u001b[32m✔\u001b[39m \u001b[34mstringr\u001b[39m 1.4.0\n",
      "\u001b[32m✔\u001b[39m \u001b[34mreadr  \u001b[39m 1.3.1     \u001b[32m✔\u001b[39m \u001b[34mforcats\u001b[39m 0.4.0\n",
      "── \u001b[1mConflicts\u001b[22m ────────────────────────────────────────── tidyverse_conflicts() ──\n",
      "\u001b[31m✖\u001b[39m \u001b[34mdplyr\u001b[39m::\u001b[32mfilter()\u001b[39m masks \u001b[34mstats\u001b[39m::filter()\n",
      "\u001b[31m✖\u001b[39m \u001b[34mdplyr\u001b[39m::\u001b[32mlag()\u001b[39m    masks \u001b[34mstats\u001b[39m::lag()\n"
     ]
    }
   ],
   "source": [
    "library(tidyverse)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "options(repr.plot.width=4, repr.plot.height=3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Parsed with column specification:\n",
      "cols(\n",
      "  .default = col_double(),\n",
      "  Label = \u001b[31mcol_character()\u001b[39m,\n",
      "  Media = \u001b[31mcol_character()\u001b[39m,\n",
      "  Strain = \u001b[31mcol_character()\u001b[39m\n",
      ")\n",
      "See spec(...) for full column specifications.\n"
     ]
    }
   ],
   "source": [
    "data <- read_tsv('data/gene_counts_raw.txt')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**0**. The `Label` column has 3 pieces of information `Sample`, `Method` andd `Person` in a single cell. Fix this and save the tidy DataFrame as `df`."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**1**. Plot a scatter plot of gene100 against gene 1001. Color points by the method used. Save the image as a PNG file 'fig1.png' in the 'figs' folder."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"figs/fig1.png\" alt=\"Fig1\" width=400>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**2**. Make a boxplot plot of gene100 counts by method."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"figs/fig2.png\" alt=\"Fig2\" width=400>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**3**. Make a jitter plot of gene100 counts by Media and color the points by method. Set the jitter width to be 0.2."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"figs/fig3.png\" alt=\"Fig3\" width=400>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**4**. Make a grid of histograms of counts for gene100, with rows showing the person and columns showing the method used."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"figs/fig4.png\" alt=\"Fig4\" width=400>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**5**. Make a row of boxplots of log counts of the top 5 genes where each column shows a different method.\n",
    "\n",
    "**Warning**: This involves quite a bit of data processing."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<img src=\"figs/fig5.png\" alt=\"Fig5\" width=400>"
   ]
  }
 ],
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