SteadyStates.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Find Steady states of rtgM4"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "using Pkg \n",
    "Pkg.activate(\"SteadyStates\")\n",
    "Pkg.instantiate();"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "using RetroSignalModel\n",
    "using Parameters\n",
    "using FindSteadyStates\n",
    "using CSV, DataFrames\n",
    "using ProgressBars\n",
    "using Random\n",
    "using SteadyStateDiffEq\n",
    "using LaTeXStrings\n",
    "using SteadyStates: mergeCSV, create_null_dataframe, find_undef_name, valid\n",
    "\n",
    "import RetroSignalModel as rs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Model\n",
    "\n",
    "- `rtgM4`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "rtgM4 = rs.rtgM4(1)\n",
    "model = rtgM4.model\n",
    "param = (;p=rtgM4.p, u=rtgM4.u) \n",
    "\n",
    "de = DEsteady(func=model, u0= param.u, p= param.p, method= SSRootfind());"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Find Steady States\n",
    "\n",
    "Start searching steady states:\n",
    "1. use `SSRootfind` for both stable and unstable points\n",
    "\n",
    "\n",
    "### Storage\n",
    "- `SteadyStates/data/`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"SteadyStates/data/steady_states_\""
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "savedir =  joinpath(\"SteadyStates/data/steady_states_\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# For Saving to Datafreme. \n",
    "if false\n",
    "\n",
    "    ks = keys(param.u)\n",
    "    filename = joinpath(save_dir, \"steady_states_PLACEHOLDER.csv\")\n",
    "\n",
    "    # number of iteration\n",
    "    ind = Int(64800)\n",
    "    iter_number = 10\n",
    "\n",
    "    for i in ProgressBar(1:iter_number)\n",
    "\n",
    "        df = create_null_dataframe(ks) # renew df. Clear the memory\n",
    "\n",
    "        param_ranges = [  \n",
    "            0.:1.,\n",
    "            100.:1000.,\n",
    "            0.:100.,\n",
    "            0.:1.,\n",
    "            0.:10.,\n",
    "            100.:10000.,\n",
    "            0.:1000.,\n",
    "            0.:10.,\n",
    "            0.:100.,\n",
    "            0.:1000.,\n",
    "            0.:100.,\n",
    "            0.:100.,\n",
    "            0.:10.,\n",
    "            0.:100.,\n",
    "            0.:100.,\n",
    "            0.:100.,\n",
    "            0.:10.,\n",
    "        ]\n",
    "\n",
    "        pr = ParameterRandom(\n",
    "            param_ranges,\n",
    "            len = ind)\n",
    "\n",
    "        sols = solve(de, pr);\n",
    "\n",
    "\n",
    "        for u in sols.u\n",
    "            any(isnan, u) ? continue : nothing # skip NaN value\n",
    "            d = Dict(keys(param.u) .=> u)\n",
    "            push!(df,d)\n",
    "        end\n",
    "\n",
    "\n",
    "\n",
    "        csvname = find_undef_name(filename, \"PLACEHOLDER\")\n",
    "\n",
    "        nrow(df) == 0 ? nothing : CSV.write(csvname, df) # skip null dataframe\n",
    "\n",
    "    end\n",
    "end "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Merge files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "\"SteadyStates/data/valid_ss.csv\""
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = mergeCSV(savedir);\n",
    "\n",
    "df_ = valid(df; low=0.,high=1e4, s_low=0., s_high=1.0) # valid dataset\n",
    "sort!(df_)\n",
    "CSV.write(joinpath(\"SteadyStates/data\", \"valid_ss.csv\"),df_)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table class=\"data-frame\"><thead><tr><th></th><th>Bmh</th><th>BmhMks</th><th>Mks</th><th>Rtg13_a_c</th><th>Rtg13_a_n</th><th>Rtg13_i_c</th><th>Rtg13_i_n</th><th>Rtg1_c</th></tr><tr><th></th><th>Float64</th><th>Float64</th><th>Float64</th><th>Float64</th><th>Float64</th><th>Float64</th><th>Float64</th><th>Float64</th></tr></thead><tbody><p>725 rows × 17 columns (omitted printing of 9 columns)</p><tr><th>1</th><td>7308.61</td><td>109.906</td><td>0.615391</td><td>0.0652567</td><td>0.173116</td><td>7.57005</td><td>2.92808</td><td>1.52829</td></tr><tr><th>2</th><td>8647.37</td><td>145.583</td><td>0.688956</td><td>0.759752</td><td>2.10235</td><td>1470.42</td><td>201.717</td><td>26.3655</td></tr><tr><th>3</th><td>2285.03</td><td>25.6052</td><td>0.458563</td><td>0.41964</td><td>0.731933</td><td>101.543</td><td>20.7792</td><td>5.46277</td></tr><tr><th>4</th><td>7048.75</td><td>291.425</td><td>1.69192</td><td>0.527703</td><td>1.56541</td><td>2982.16</td><td>377.687</td><td>71.5453</td></tr><tr><th>5</th><td>7545.26</td><td>394.107</td><td>2.13749</td><td>0.07292</td><td>0.220481</td><td>3024.23</td><td>367.105</td><td>515.038</td></tr><tr><th>6</th><td>5354.27</td><td>111.566</td><td>0.852701</td><td>0.085788</td><td>0.228152</td><td>21.8763</td><td>5.29331</td><td>3.51247</td></tr><tr><th>7</th><td>4584.02</td><td>0.567586</td><td>0.00506699</td><td>5.86037</td><td>1.91219</td><td>511.751</td><td>84.5695</td><td>45.9478</td></tr><tr><th>8</th><td>8938.89</td><td>193.247</td><td>0.884693</td><td>0.088391</td><td>0.252937</td><td>37.7941</td><td>7.4998</td><td>5.50624</td></tr><tr><th>9</th><td>7194.8</td><td>227.161</td><td>1.29205</td><td>0.0798471</td><td>0.232118</td><td>4.13382</td><td>3.19992</td><td>0.535395</td></tr><tr><th>10</th><td>702.703</td><td>0.716937</td><td>0.0417516</td><td>0.199052</td><td>0.0682534</td><td>2.64642</td><td>1.13457</td><td>5.44151</td></tr><tr><th>11</th><td>9085.57</td><td>209.504</td><td>0.943637</td><td>0.0194072</td><td>0.0559899</td><td>4.9082</td><td>1.24332</td><td>3.17147</td></tr><tr><th>12</th><td>6810.37</td><td>99.0978</td><td>0.595467</td><td>0.0391603</td><td>0.102023</td><td>7.68851</td><td>2.11471</td><td>2.73801</td></tr><tr><th>13</th><td>9261.27</td><td>105.622</td><td>0.46671</td><td>0.160397</td><td>0.422634</td><td>558.332</td><td>72.222</td><td>50.1841</td></tr><tr><th>14</th><td>7187.52</td><td>117.523</td><td>0.669126</td><td>0.178203</td><td>0.477949</td><td>114.591</td><td>19.3773</td><td>8.97864</td></tr><tr><th>15</th><td>8259.38</td><td>2.17647</td><td>0.0107837</td><td>0.928869</td><td>0.460313</td><td>216.999</td><td>31.6075</td><td>34.0774</td></tr><tr><th>16</th><td>4679.08</td><td>33.5268</td><td>0.293222</td><td>0.103641</td><td>0.201141</td><td>30.2087</td><td>5.98658</td><td>5.81884</td></tr><tr><th>17</th><td>8338.41</td><td>37.0857</td><td>0.182007</td><td>0.145811</td><td>0.293483</td><td>14.9755</td><td>5.2264</td><td>1.87583</td></tr><tr><th>18</th><td>2069.98</td><td>39.5002</td><td>0.780902</td><td>1.49853</td><td>3.08264</td><td>2635.35</td><td>353.596</td><td>33.4661</td></tr><tr><th>19</th><td>9207.33</td><td>47.7395</td><td>0.212182</td><td>0.0276693</td><td>0.0604932</td><td>0.993231</td><td>0.824632</td><td>0.503655</td></tr><tr><th>20</th><td>7654.83</td><td>179.295</td><td>0.958512</td><td>0.112345</td><td>0.318889</td><td>11.8608</td><td>5.14157</td><td>1.26959</td></tr><tr><th>21</th><td>2739.83</td><td>68.0986</td><td>1.01713</td><td>0.064742</td><td>0.155873</td><td>98.6646</td><td>13.7085</td><td>24.2274</td></tr><tr><th>22</th><td>4738.98</td><td>12.1793</td><td>0.105173</td><td>0.412837</td><td>0.503856</td><td>110.677</td><td>19.2343</td><td>9.45369</td></tr><tr><th>23</th><td>1039.77</td><td>0.133162</td><td>0.00524089</td><td>0.266663</td><td>0.0738363</td><td>0.0476136</td><td>0.894205</td><td>0.18527</td></tr><tr><th>24</th><td>8283.11</td><td>90.6614</td><td>0.447912</td><td>0.204896</td><td>0.524935</td><td>177.667</td><td>27.5286</td><td>12.7963</td></tr><tr><th>25</th><td>6188.25</td><td>38.9338</td><td>0.257468</td><td>0.606714</td><td>1.24194</td><td>924.912</td><td>125.965</td><td>29.1568</td></tr><tr><th>26</th><td>5775.28</td><td>299.243</td><td>2.12039</td><td>0.114846</td><td>0.341331</td><td>14.1405</td><td>5.67694</td><td>1.42249</td></tr><tr><th>27</th><td>3535.87</td><td>11.9489</td><td>0.138291</td><td>1.03809</td><td>1.2542</td><td>583.587</td><td>85.0161</td><td>20.2352</td></tr><tr><th>28</th><td>8889.36</td><td>89.4936</td><td>0.411989</td><td>0.924505</td><td>2.36253</td><td>2346.91</td><td>310.406</td><td>37.8322</td></tr><tr><th>29</th><td>5511.49</td><td>67.7868</td><td>0.503315</td><td>1.62047</td><td>3.89714</td><td>1704.47</td><td>250.848</td><td>16.7004</td></tr><tr><th>30</th><td>8182.0</td><td>22.3843</td><td>0.111956</td><td>1.043</td><td>1.71629</td><td>3166.07</td><td>401.668</td><td>75.1096</td></tr><tr><th>&vellip;</th><td>&vellip;</td><td>&vellip;</td><td>&vellip;</td><td>&vellip;</td><td>&vellip;</td><td>&vellip;</td><td>&vellip;</td><td>&vellip;</td></tr></tbody></table>"
      ],
      "text/latex": [
       "\\begin{tabular}{r|ccccccccc}\n",
       "\t& Bmh & BmhMks & Mks & Rtg13\\_a\\_c & Rtg13\\_a\\_n & Rtg13\\_i\\_c & Rtg13\\_i\\_n & Rtg1\\_c & \\\\\n",
       "\t\\hline\n",
       "\t& Float64 & Float64 & Float64 & Float64 & Float64 & Float64 & Float64 & Float64 & \\\\\n",
       "\t\\hline\n",
       "\t1 & 7308.61 & 109.906 & 0.615391 & 0.0652567 & 0.173116 & 7.57005 & 2.92808 & 1.52829 & $\\dots$ \\\\\n",
       "\t2 & 8647.37 & 145.583 & 0.688956 & 0.759752 & 2.10235 & 1470.42 & 201.717 & 26.3655 & $\\dots$ \\\\\n",
       "\t3 & 2285.03 & 25.6052 & 0.458563 & 0.41964 & 0.731933 & 101.543 & 20.7792 & 5.46277 & $\\dots$ \\\\\n",
       "\t4 & 7048.75 & 291.425 & 1.69192 & 0.527703 & 1.56541 & 2982.16 & 377.687 & 71.5453 & $\\dots$ \\\\\n",
       "\t5 & 7545.26 & 394.107 & 2.13749 & 0.07292 & 0.220481 & 3024.23 & 367.105 & 515.038 & $\\dots$ \\\\\n",
       "\t6 & 5354.27 & 111.566 & 0.852701 & 0.085788 & 0.228152 & 21.8763 & 5.29331 & 3.51247 & $\\dots$ \\\\\n",
       "\t7 & 4584.02 & 0.567586 & 0.00506699 & 5.86037 & 1.91219 & 511.751 & 84.5695 & 45.9478 & $\\dots$ \\\\\n",
       "\t8 & 8938.89 & 193.247 & 0.884693 & 0.088391 & 0.252937 & 37.7941 & 7.4998 & 5.50624 & $\\dots$ \\\\\n",
       "\t9 & 7194.8 & 227.161 & 1.29205 & 0.0798471 & 0.232118 & 4.13382 & 3.19992 & 0.535395 & $\\dots$ \\\\\n",
       "\t10 & 702.703 & 0.716937 & 0.0417516 & 0.199052 & 0.0682534 & 2.64642 & 1.13457 & 5.44151 & $\\dots$ \\\\\n",
       "\t11 & 9085.57 & 209.504 & 0.943637 & 0.0194072 & 0.0559899 & 4.9082 & 1.24332 & 3.17147 & $\\dots$ \\\\\n",
       "\t12 & 6810.37 & 99.0978 & 0.595467 & 0.0391603 & 0.102023 & 7.68851 & 2.11471 & 2.73801 & $\\dots$ \\\\\n",
       "\t13 & 9261.27 & 105.622 & 0.46671 & 0.160397 & 0.422634 & 558.332 & 72.222 & 50.1841 & $\\dots$ \\\\\n",
       "\t14 & 7187.52 & 117.523 & 0.669126 & 0.178203 & 0.477949 & 114.591 & 19.3773 & 8.97864 & $\\dots$ \\\\\n",
       "\t15 & 8259.38 & 2.17647 & 0.0107837 & 0.928869 & 0.460313 & 216.999 & 31.6075 & 34.0774 & $\\dots$ \\\\\n",
       "\t16 & 4679.08 & 33.5268 & 0.293222 & 0.103641 & 0.201141 & 30.2087 & 5.98658 & 5.81884 & $\\dots$ \\\\\n",
       "\t17 & 8338.41 & 37.0857 & 0.182007 & 0.145811 & 0.293483 & 14.9755 & 5.2264 & 1.87583 & $\\dots$ \\\\\n",
       "\t18 & 2069.98 & 39.5002 & 0.780902 & 1.49853 & 3.08264 & 2635.35 & 353.596 & 33.4661 & $\\dots$ \\\\\n",
       "\t19 & 9207.33 & 47.7395 & 0.212182 & 0.0276693 & 0.0604932 & 0.993231 & 0.824632 & 0.503655 & $\\dots$ \\\\\n",
       "\t20 & 7654.83 & 179.295 & 0.958512 & 0.112345 & 0.318889 & 11.8608 & 5.14157 & 1.26959 & $\\dots$ \\\\\n",
       "\t21 & 2739.83 & 68.0986 & 1.01713 & 0.064742 & 0.155873 & 98.6646 & 13.7085 & 24.2274 & $\\dots$ \\\\\n",
       "\t22 & 4738.98 & 12.1793 & 0.105173 & 0.412837 & 0.503856 & 110.677 & 19.2343 & 9.45369 & $\\dots$ \\\\\n",
       "\t23 & 1039.77 & 0.133162 & 0.00524089 & 0.266663 & 0.0738363 & 0.0476136 & 0.894205 & 0.18527 & $\\dots$ \\\\\n",
       "\t24 & 8283.11 & 90.6614 & 0.447912 & 0.204896 & 0.524935 & 177.667 & 27.5286 & 12.7963 & $\\dots$ \\\\\n",
       "\t25 & 6188.25 & 38.9338 & 0.257468 & 0.606714 & 1.24194 & 924.912 & 125.965 & 29.1568 & $\\dots$ \\\\\n",
       "\t26 & 5775.28 & 299.243 & 2.12039 & 0.114846 & 0.341331 & 14.1405 & 5.67694 & 1.42249 & $\\dots$ \\\\\n",
       "\t27 & 3535.87 & 11.9489 & 0.138291 & 1.03809 & 1.2542 & 583.587 & 85.0161 & 20.2352 & $\\dots$ \\\\\n",
       "\t28 & 8889.36 & 89.4936 & 0.411989 & 0.924505 & 2.36253 & 2346.91 & 310.406 & 37.8322 & $\\dots$ \\\\\n",
       "\t29 & 5511.49 & 67.7868 & 0.503315 & 1.62047 & 3.89714 & 1704.47 & 250.848 & 16.7004 & $\\dots$ \\\\\n",
       "\t30 & 8182.0 & 22.3843 & 0.111956 & 1.043 & 1.71629 & 3166.07 & 401.668 & 75.1096 & $\\dots$ \\\\\n",
       "\t$\\dots$ & $\\dots$ & $\\dots$ & $\\dots$ & $\\dots$ & $\\dots$ & $\\dots$ & $\\dots$ & $\\dots$ &  \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/plain": [
       "\u001b[1m725×17 DataFrame\u001b[0m\n",
       "\u001b[1m Row \u001b[0m│\u001b[1m Bmh      \u001b[0m\u001b[1m BmhMks       \u001b[0m\u001b[1m Mks         \u001b[0m\u001b[1m Rtg13_a_c \u001b[0m\u001b[1m Rtg13_a_n \u001b[0m\u001b[1m Rtg13_i_c   \u001b[0m ⋯\n",
       "\u001b[1m     \u001b[0m│\u001b[90m Float64  \u001b[0m\u001b[90m Float64      \u001b[0m\u001b[90m Float64     \u001b[0m\u001b[90m Float64   \u001b[0m\u001b[90m Float64   \u001b[0m\u001b[90m Float64     \u001b[0m ⋯\n",
       "─────┼──────────────────────────────────────────────────────────────────────────\n",
       "   1 │ 7308.61   109.906       0.615391     0.0652567  0.173116      7.57005   ⋯\n",
       "   2 │ 8647.37   145.583       0.688956     0.759752   2.10235    1470.42\n",
       "   3 │ 2285.03    25.6052      0.458563     0.41964    0.731933    101.543\n",
       "   4 │ 7048.75   291.425       1.69192      0.527703   1.56541    2982.16\n",
       "   5 │ 7545.26   394.107       2.13749      0.07292    0.220481   3024.23      ⋯\n",
       "   6 │ 5354.27   111.566       0.852701     0.085788   0.228152     21.8763\n",
       "   7 │ 4584.02     0.567586    0.00506699   5.86037    1.91219     511.751\n",
       "   8 │ 8938.89   193.247       0.884693     0.088391   0.252937     37.7941\n",
       "   9 │ 7194.8    227.161       1.29205      0.0798471  0.232118      4.13382   ⋯\n",
       "  10 │  702.703    0.716937    0.0417516    0.199052   0.0682534     2.64642\n",
       "  11 │ 9085.57   209.504       0.943637     0.0194072  0.0559899     4.9082\n",
       "  ⋮  │    ⋮           ⋮             ⋮           ⋮          ⋮           ⋮       ⋱\n",
       " 716 │  685.063    2.52124     0.150608     2.89688    1.53324    1050.75\n",
       " 717 │ 7954.11     6.55044     0.033701     6.32625    5.49661    1746.66      ⋯\n",
       " 718 │ 4082.41     0.646597    0.00648159   0.774718   0.259607     69.4763\n",
       " 719 │  310.325    0.00164977  0.000217557  6.67488    1.74614       2.98951\n",
       " 720 │ 4917.77    66.7097      0.555118     0.0171328  0.0410437    26.5822\n",
       " 721 │  911.14     1.06699     0.0479226    0.040104   0.015282      0.0240173 ⋯\n",
       " 722 │ 9878.36    89.762       0.371854     0.0224979  0.0575262     5.13322\n",
       " 723 │  228.359    0.430979    0.0772328    0.555668   0.172779     65.8563\n",
       " 724 │ 4949.76    12.5117      0.103441     0.905834   1.12137    2182.86\n",
       " 725 │ 5831.33   154.902       1.08706      0.48523    1.35357     851.284     ⋯\n",
       "\u001b[31m                                                 11 columns and 704 rows omitted\u001b[0m"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_ = valid(df; low=0.,high=1e4, s_low=0., s_high=1.0) # valid dataset"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Plot Steady States Results in Different Conditions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001b[32m\u001b[1m Activating\u001b[22m\u001b[39m environment at `~/project/MitoRetrogradeModel/MitoChannelAnalysis/SteadyStates/Project.toml`\n"
     ]
    }
   ],
   "source": [
    "using Pkg \n",
    "Pkg.activate(\"SteadyStates\")\n",
    "Pkg.instantiate()\n",
    "using IJulia\n",
    "using TikzPictures\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "ename": "LoadError",
     "evalue": "SystemError: opening file \"./jl_nLWelh/texput.log\": No such file or directory",
     "output_type": "error",
     "traceback": [
      "SystemError: opening file \"./jl_nLWelh/texput.log\": No such file or directory",
      "",
      "Stacktrace:",
      " [1] systemerror(::String, ::Int32; extrainfo::Nothing) at ./error.jl:168",
      " [2] #systemerror#48 at ./error.jl:167 [inlined]",
      " [3] systemerror at ./error.jl:167 [inlined]",
      " [4] open(::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing) at ./iostream.jl:284",
      " [5] open at ./iostream.jl:273 [inlined]",
      " [6] open(::Base.var\"#296#297\"{String}, ::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at ./io.jl:323",
      " [7] open at ./io.jl:323 [inlined]",
      " [8] read at ./io.jl:410 [inlined]",
      " [9] (::TikzPictures.var\"#17#18\"{PDF,TikzPicture,String})() at /home/ubuntu/.julia/packages/TikzPictures/161Ck/src/TikzPictures.jl:273",
      " [10] cd(::TikzPictures.var\"#17#18\"{PDF,TikzPicture,String}, ::String) at ./file.jl:104",
      " [11] save(::PDF, ::TikzPicture) at /home/ubuntu/.julia/packages/TikzPictures/161Ck/src/TikzPictures.jl:252",
      " [12] top-level scope at In[5]:2",
      " [13] include_string(::Function, ::Module, ::String, ::String) at ./loading.jl:1091"
     ]
    }
   ],
   "source": [
    "tp = TikzPicture(\"\\\\draw (0,0) -- (10,10);\\n\\\\draw (10,0) -- (0,10);\\n\\\\node at (5,5) {tikz \\$\\\\sqrt{\\\\pi}\\$};\", options=\"scale=0.25\", preamble=\"\")\n",
    "save(PDF(\"test\"), tp)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "\"\"\"\n",
    "Try conditions of the model with given initial variables and parameters.\n",
    "\"\"\"\n",
    "function Try_conditions(u,p, VALID_SETTING;\n",
    "                        BREAK=false,\n",
    "                        Cond_Random=false)\n",
    "\n",
    "        @unpack  model, S_SPAN, DEL_CONC, TRANS_THRESHOLD,  SSMETHOD, cond, protein_lookup = VALID_SETTING\n",
    "\n",
    "        valid = 1\n",
    "\n",
    "        num_cond = size(cond)[1] # number of conditions\n",
    "\n",
    "        # Shuffling the conditions\n",
    "        trial_cond_order = Cond_Random ? shuffle(1:num_cond) : 1:num_cond\n",
    "\n",
    "        test_log = Dict(\"nuc\"=>[], \"cyt\"=>[])\n",
    "\n",
    "        # get initial condition\n",
    "        de = DEsteady(func=model, u0=u, p=p, method=SSMETHOD)\n",
    "        #u_ = solve(de) # This step changed the initial value, and reset as the steady ones\n",
    "        u_ = redist2monomer(u, protein_lookup)\n",
    "\n",
    "        for trial_n in trial_cond_order # Test conditions\n",
    "\n",
    "            con = cond[trial_n,:]\n",
    "\n",
    "            if typeof(con.Trans2Nuc) == Missing \n",
    "                push!(test_log[\"nuc\"] , Missing)\n",
    "                push!(test_log[\"cyt\"], Missing)\n",
    "                continue  # some conditions are not measured\n",
    "            end\n",
    "            \n",
    "\n",
    "            ud = Get_del_u(u_, con.rtg1, con.rtg2, con.rtg3, con.mks, con.s, protein_lookup; del_conc=DEL_CONC, s_span=S_SPAN)\n",
    "\n",
    "            sol = solve(de(ud))\n",
    "\n",
    "            # Check the steady-state is real\n",
    "            if sol.retcode==:Failure\n",
    "                valid = 0 #unstable system\n",
    "                break\n",
    "            end\n",
    "\n",
    "\n",
    "            trans2nuc = Get_output(sol, con.gfp, protein_lookup, threshold=TRANS_THRESHOLD) # 1 means nucleus has significantly higer concentration than cytosol\n",
    "\n",
    "            \n",
    "  \n",
    "            push!(test_log[\"nuc\"] , trans2nuc[1])\n",
    "            push!(test_log[\"cyt\"], trans2nuc[2])\n",
    "            \n",
    " \n",
    "    end\n",
    "    \n",
    "        return test_log\n",
    "end\n",
    "\n",
    "\n",
    "function Get_output(sol, gfp, protein_lookup; threshold = TRANS_THRESHOLD)\n",
    "\n",
    "    if gfp == \"rtg1\"\n",
    "        cyt_index = protein_lookup[:Rtg1_c]\n",
    "        nuc_index = protein_lookup[:Rtg1_n]\n",
    "    elseif gfp == \"rtg3\"\n",
    "        cyt_index = protein_lookup[:Rtg3_c]\n",
    "        nuc_index = protein_lookup[:Rtg3_n]\n",
    "    else\n",
    "        throw(MathodError)\n",
    "    end\n",
    "\n",
    "    total_conc_cyt = sum(sol[cyt_index])\n",
    "    total_conc_nuc = sum(sol[nuc_index])\n",
    "\n",
    "  \n",
    "    return (total_conc_nuc, total_conc_cyt)\n",
    "end\n",
    "\n",
    "function Get_del_u(u, rtg1, rtg2, rtg3, mks, s, protein_lookup; del_conc=DEL_CONC, s_span=S_SPAN )\n",
    "\n",
    "    del_info = Dict([:Rtg1, :Rtg2, :Rtg3, :Mks] .=> [rtg1, rtg2, rtg3, mks])\n",
    "    ud = deepcopy(u)\n",
    "\n",
    "    for protein in keys(del_info)\n",
    "        protein_existence = del_info[protein]\n",
    "        if protein_existence == 0\n",
    "            ud[protein_lookup[protein]] .= del_conc\n",
    "        end\n",
    "    end\n",
    "\n",
    "    ud[protein_lookup[:s]] = s_span[s+1] #in boolean, s=0 means 1 in span_tuple\n",
    "\n",
    "    return ud\n",
    "end\n",
    "\n",
    "\n",
    "function redist2monomer(u, protein_lookup)\n",
    "    u_dist = zeros(length(u))\n",
    "    \n",
    "    \n",
    "    # Rtg2 \n",
    "    sum_rtg2 = sum(u[protein_lookup[:Rtg2]])\n",
    "    u_dist[2] = sum_rtg2\n",
    "    \n",
    "     # Rtg3\n",
    "    sum_rtg3 = sum(u[protein_lookup[:Rtg3]])\n",
    "    u_dist[11] = sum_rtg3\n",
    "    \n",
    "     # Rtg1\n",
    "    sum_rtg1 = sum(u[protein_lookup[:Rtg1]])\n",
    "    u_dist[14] = sum_rtg1\n",
    "    \n",
    "    # Mks\n",
    "    sum_mks = sum(u[protein_lookup[:Mks]])\n",
    "    u_dist[4] = sum_mks\n",
    "    \n",
    "    # Bmh \n",
    "    sum_bmh = sum(u[protein_lookup[:Bmh]])\n",
    "    u_dist[6] = sum_bmh\n",
    "    \n",
    "    return u_dist\n",
    "    \n",
    "end\n",
    "\n",
    "param = RetroSignalModel.rtgM4.param();\n",
    "model = RetroSignalModel.rtgM4.model;\n",
    "u = param.u; \n",
    "p = param.p;"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[37ms(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n",
      "\u001b[37mRtg2_ina_c(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  651.6543766184084\n",
      "\u001b[37mRtg2_act_c(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n",
      "\u001b[37mMks(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  267.49672022463324\n",
      "\u001b[37mRtg2Mks_c(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n",
      "\u001b[37mBmh(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  10000.000000000005\n",
      "\u001b[37mBmhMks(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n",
      "\u001b[37mRtg13_a_c(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n",
      "\u001b[37mRtg13_i_c(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n",
      "\u001b[37mRtg3_i_c(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n",
      "\u001b[37mRtg3_a_c(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  409.5036119882923\n",
      "\u001b[37mRtg3_a_n(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n",
      "\u001b[37mRtg3_i_n(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n",
      "\u001b[37mRtg1_c(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  145.92035635683752\n",
      "\u001b[37mRtg1_n(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n",
      "\u001b[37mRtg13_a_n(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n",
      "\u001b[37mRtg13_i_n(\u001b[39m\u001b[37mt\u001b[39m\u001b[37m)\u001b[39m  0.0\n"
     ]
    }
   ],
   "source": [
    "u_sep = redist2monomer(u,RetroSignalModel.get_protein_lookup(model))\n",
    "for (j,i) in zip(u_sep, model.states)\n",
    "    println(i,\"  \",j)\n",
    "end"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Dict{String,Array{Any,1}} with 2 entries:\n",
       "  \"cyt\" => Any[Missing, 43.3458, 43.3458, 43.3451, 193.737, 193.737, 193.737, 6…\n",
       "  \"nuc\" => Any[Missing, 366.158, 366.158, 366.159, 215.766, 215.766, 215.766, 3…"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "transRes = Try_conditions(u_sep,p, valid_setting(model))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table class=\"data-frame\"><thead><tr><th></th><th>cyt</th><th>nuc</th></tr><tr><th></th><th>Any</th><th>Any</th></tr></thead><tbody><p>20 rows × 2 columns</p><tr><th>1</th><td>Missing</td><td>Missing</td></tr><tr><th>2</th><td>43.3458</td><td>366.158</td></tr><tr><th>3</th><td>43.3458</td><td>366.158</td></tr><tr><th>4</th><td>43.3451</td><td>366.159</td></tr><tr><th>5</th><td>193.737</td><td>215.766</td></tr><tr><th>6</th><td>193.737</td><td>215.766</td></tr><tr><th>7</th><td>193.737</td><td>215.766</td></tr><tr><th>8</th><td>63.2278</td><td>346.276</td></tr><tr><th>9</th><td>Missing</td><td>Missing</td></tr><tr><th>10</th><td>Missing</td><td>Missing</td></tr><tr><th>11</th><td>145.843</td><td>0.078209</td></tr><tr><th>12</th><td>145.842</td><td>0.0784535</td></tr><tr><th>13</th><td>91.0302</td><td>54.8902</td></tr><tr><th>14</th><td>91.0302</td><td>54.8902</td></tr><tr><th>15</th><td>91.0303</td><td>54.8901</td></tr><tr><th>16</th><td>35.5487</td><td>110.372</td></tr><tr><th>17</th><td>61.8543</td><td>347.649</td></tr><tr><th>18</th><td>61.8543</td><td>347.649</td></tr><tr><th>19</th><td>34.8564</td><td>111.064</td></tr><tr><th>20</th><td>34.8564</td><td>111.064</td></tr></tbody></table>"
      ],
      "text/latex": [
       "\\begin{tabular}{r|cc}\n",
       "\t& cyt & nuc\\\\\n",
       "\t\\hline\n",
       "\t& Any & Any\\\\\n",
       "\t\\hline\n",
       "\t1 & Missing & Missing \\\\\n",
       "\t2 & 43.3458 & 366.158 \\\\\n",
       "\t3 & 43.3458 & 366.158 \\\\\n",
       "\t4 & 43.3451 & 366.159 \\\\\n",
       "\t5 & 193.737 & 215.766 \\\\\n",
       "\t6 & 193.737 & 215.766 \\\\\n",
       "\t7 & 193.737 & 215.766 \\\\\n",
       "\t8 & 63.2278 & 346.276 \\\\\n",
       "\t9 & Missing & Missing \\\\\n",
       "\t10 & Missing & Missing \\\\\n",
       "\t11 & 145.843 & 0.078209 \\\\\n",
       "\t12 & 145.842 & 0.0784535 \\\\\n",
       "\t13 & 91.0302 & 54.8902 \\\\\n",
       "\t14 & 91.0302 & 54.8902 \\\\\n",
       "\t15 & 91.0303 & 54.8901 \\\\\n",
       "\t16 & 35.5487 & 110.372 \\\\\n",
       "\t17 & 61.8543 & 347.649 \\\\\n",
       "\t18 & 61.8543 & 347.649 \\\\\n",
       "\t19 & 34.8564 & 111.064 \\\\\n",
       "\t20 & 34.8564 & 111.064 \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/plain": [
       "\u001b[1m20×2 DataFrame\u001b[0m\n",
       "\u001b[1m Row \u001b[0m│\u001b[1m cyt     \u001b[0m\u001b[1m nuc       \u001b[0m\n",
       "\u001b[1m     \u001b[0m│\u001b[90m Any     \u001b[0m\u001b[90m Any       \u001b[0m\n",
       "─────┼────────────────────\n",
       "   1 │ Missing  Missing\n",
       "   2 │ 43.3458  366.158\n",
       "   3 │ 43.3458  366.158\n",
       "   4 │ 43.3451  366.159\n",
       "   5 │ 193.737  215.766\n",
       "   6 │ 193.737  215.766\n",
       "   7 │ 193.737  215.766\n",
       "   8 │ 63.2278  346.276\n",
       "   9 │ Missing  Missing\n",
       "  10 │ Missing  Missing\n",
       "  11 │ 145.843  0.078209\n",
       "  12 │ 145.842  0.0784535\n",
       "  13 │ 91.0302  54.8902\n",
       "  14 │ 91.0302  54.8902\n",
       "  15 │ 91.0303  54.8901\n",
       "  16 │ 35.5487  110.372\n",
       "  17 │ 61.8543  347.649\n",
       "  18 │ 61.8543  347.649\n",
       "  19 │ 34.8564  111.064\n",
       "  20 │ 34.8564  111.064"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = DataFrame(transRes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "651.6543766184084"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Rtg2 = sum(u[RetroSignalModel.get_protein_lookup(model)[:Rtg2]])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table class=\"data-frame\"><thead><tr><th></th><th>rtg1</th><th>rtg2</th><th>rtg3</th><th>s</th><th>mks</th><th>gfp</th><th>Trans2Nuc</th></tr><tr><th></th><th>Int64</th><th>Int64</th><th>Int64</th><th>Int64</th><th>Int64</th><th>String</th><th>Int64?</th></tr></thead><tbody><p>20 rows × 7 columns</p><tr><th>1</th><td>0</td><td>0</td><td>1</td><td>0</td><td>1</td><td>rtg3</td><td><em>missing</em></td></tr><tr><th>2</th><td>0</td><td>0</td><td>1</td><td>1</td><td>1</td><td>rtg3</td><td>1</td></tr><tr><th>3</th><td>0</td><td>1</td><td>1</td><td>0</td><td>1</td><td>rtg3</td><td>1</td></tr><tr><th>4</th><td>0</td><td>1</td><td>1</td><td>1</td><td>1</td><td>rtg3</td><td>1</td></tr><tr><th>5</th><td>1</td><td>0</td><td>1</td><td>0</td><td>1</td><td>rtg3</td><td>0</td></tr><tr><th>6</th><td>1</td><td>0</td><td>1</td><td>1</td><td>1</td><td>rtg3</td><td>0</td></tr><tr><th>7</th><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>rtg3</td><td>0</td></tr><tr><th>8</th><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>rtg3</td><td>1</td></tr><tr><th>9</th><td>1</td><td>0</td><td>0</td><td>0</td><td>1</td><td>rtg1</td><td><em>missing</em></td></tr><tr><th>10</th><td>1</td><td>0</td><td>0</td><td>1</td><td>1</td><td>rtg1</td><td><em>missing</em></td></tr><tr><th>11</th><td>1</td><td>1</td><td>0</td><td>0</td><td>1</td><td>rtg1</td><td>0</td></tr><tr><th>12</th><td>1</td><td>1</td><td>0</td><td>1</td><td>1</td><td>rtg1</td><td>0</td></tr><tr><th>13</th><td>1</td><td>0</td><td>1</td><td>0</td><td>1</td><td>rtg1</td><td>0</td></tr><tr><th>14</th><td>1</td><td>0</td><td>1</td><td>1</td><td>1</td><td>rtg1</td><td>0</td></tr><tr><th>15</th><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>rtg1</td><td>0</td></tr><tr><th>16</th><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>rtg1</td><td>1</td></tr><tr><th>17</th><td>1</td><td>0</td><td>1</td><td>0</td><td>0</td><td>rtg3</td><td>1</td></tr><tr><th>18</th><td>1</td><td>1</td><td>1</td><td>0</td><td>0</td><td>rtg3</td><td>1</td></tr><tr><th>19</th><td>1</td><td>0</td><td>1</td><td>0</td><td>0</td><td>rtg1</td><td>1</td></tr><tr><th>20</th><td>1</td><td>1</td><td>1</td><td>0</td><td>0</td><td>rtg1</td><td>1</td></tr></tbody></table>"
      ],
      "text/latex": [
       "\\begin{tabular}{r|ccccccc}\n",
       "\t& rtg1 & rtg2 & rtg3 & s & mks & gfp & Trans2Nuc\\\\\n",
       "\t\\hline\n",
       "\t& Int64 & Int64 & Int64 & Int64 & Int64 & String & Int64?\\\\\n",
       "\t\\hline\n",
       "\t1 & 0 & 0 & 1 & 0 & 1 & rtg3 & \\emph{missing} \\\\\n",
       "\t2 & 0 & 0 & 1 & 1 & 1 & rtg3 & 1 \\\\\n",
       "\t3 & 0 & 1 & 1 & 0 & 1 & rtg3 & 1 \\\\\n",
       "\t4 & 0 & 1 & 1 & 1 & 1 & rtg3 & 1 \\\\\n",
       "\t5 & 1 & 0 & 1 & 0 & 1 & rtg3 & 0 \\\\\n",
       "\t6 & 1 & 0 & 1 & 1 & 1 & rtg3 & 0 \\\\\n",
       "\t7 & 1 & 1 & 1 & 0 & 1 & rtg3 & 0 \\\\\n",
       "\t8 & 1 & 1 & 1 & 1 & 1 & rtg3 & 1 \\\\\n",
       "\t9 & 1 & 0 & 0 & 0 & 1 & rtg1 & \\emph{missing} \\\\\n",
       "\t10 & 1 & 0 & 0 & 1 & 1 & rtg1 & \\emph{missing} \\\\\n",
       "\t11 & 1 & 1 & 0 & 0 & 1 & rtg1 & 0 \\\\\n",
       "\t12 & 1 & 1 & 0 & 1 & 1 & rtg1 & 0 \\\\\n",
       "\t13 & 1 & 0 & 1 & 0 & 1 & rtg1 & 0 \\\\\n",
       "\t14 & 1 & 0 & 1 & 1 & 1 & rtg1 & 0 \\\\\n",
       "\t15 & 1 & 1 & 1 & 0 & 1 & rtg1 & 0 \\\\\n",
       "\t16 & 1 & 1 & 1 & 1 & 1 & rtg1 & 1 \\\\\n",
       "\t17 & 1 & 0 & 1 & 0 & 0 & rtg3 & 1 \\\\\n",
       "\t18 & 1 & 1 & 1 & 0 & 0 & rtg3 & 1 \\\\\n",
       "\t19 & 1 & 0 & 1 & 0 & 0 & rtg1 & 1 \\\\\n",
       "\t20 & 1 & 1 & 1 & 0 & 0 & rtg1 & 1 \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/plain": [
       "\u001b[1m20×7 DataFrame\u001b[0m\n",
       "\u001b[1m Row \u001b[0m│\u001b[1m rtg1  \u001b[0m\u001b[1m rtg2  \u001b[0m\u001b[1m rtg3  \u001b[0m\u001b[1m s     \u001b[0m\u001b[1m mks   \u001b[0m\u001b[1m gfp    \u001b[0m\u001b[1m Trans2Nuc \u001b[0m\n",
       "\u001b[1m     \u001b[0m│\u001b[90m Int64 \u001b[0m\u001b[90m Int64 \u001b[0m\u001b[90m Int64 \u001b[0m\u001b[90m Int64 \u001b[0m\u001b[90m Int64 \u001b[0m\u001b[90m String \u001b[0m\u001b[90m Int64?    \u001b[0m\n",
       "─────┼──────────────────────────────────────────────────────\n",
       "   1 │     0      0      1      0      1  rtg3   \u001b[90m   missing \u001b[0m\n",
       "   2 │     0      0      1      1      1  rtg3            1\n",
       "   3 │     0      1      1      0      1  rtg3            1\n",
       "   4 │     0      1      1      1      1  rtg3            1\n",
       "   5 │     1      0      1      0      1  rtg3            0\n",
       "   6 │     1      0      1      1      1  rtg3            0\n",
       "   7 │     1      1      1      0      1  rtg3            0\n",
       "   8 │     1      1      1      1      1  rtg3            1\n",
       "   9 │     1      0      0      0      1  rtg1   \u001b[90m   missing \u001b[0m\n",
       "  10 │     1      0      0      1      1  rtg1   \u001b[90m   missing \u001b[0m\n",
       "  11 │     1      1      0      0      1  rtg1            0\n",
       "  12 │     1      1      0      1      1  rtg1            0\n",
       "  13 │     1      0      1      0      1  rtg1            0\n",
       "  14 │     1      0      1      1      1  rtg1            0\n",
       "  15 │     1      1      1      0      1  rtg1            0\n",
       "  16 │     1      1      1      1      1  rtg1            1\n",
       "  17 │     1      0      1      0      0  rtg3            1\n",
       "  18 │     1      1      1      0      0  rtg3            1\n",
       "  19 │     1      0      1      0      0  rtg1            1\n",
       "  20 │     1      1      1      0      0  rtg1            1"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "RetroSignalModel.RTG_Response_Boolean"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/latex": [
       "\\documentclass[border={5pt 0pt 20pt 5pt}, preview]{standalone}\n",
       "\n",
       "\\usepackage{pgfplots}\n",
       "\\pgfplotsset{compat=1.15}\n",
       "\\usepackage{xcolor}\n",
       "\n",
       "\n",
       "\\usepackage{tikz}\n",
       "\\usepackage[utf8]{inputenc}\n",
       "\\usepackage{xfp}\n",
       "\\usepackage{booktabs}\n",
       "\\usetikzlibrary{calc}\n",
       "\\usepackage{graphicx}\n",
       "\n",
       "\\newcommand{\\Del}[1]{\\textit{$\\Delta$\\MakeLowercase{#1}}}\n",
       "\\newcommand\\ratio[2]{%\n",
       "    \\pgfmathparse{ #1/(#1 + #2)}\\pgfmathresult\n",
       "}\n",
       "\n",
       "\n",
       "\\newcommand\\colorBar{\n",
       "    \\begin{tikzpicture}[baseline={(0,0)}, inner sep=0,outer sep=0]\n",
       "\n",
       "       \n",
       "        \\pgfdeclarehorizontalshading{someShading}{4cm}{\n",
       "        color(0cm)=(green!0!gray);\n",
       "        color(4cm)=(green!100!gray)\n",
       "        }\n",
       "        \n",
       "        \\shade [shading=someShading, yshift=-1cm]  (0,0) rectangle ++(1,0.3);\n",
       "        \\node [] at (0,-1.3) {0};\n",
       "        \\node [] at (1,-1.3) {1};\n",
       "        \n",
       "        \\end{tikzpicture}\n",
       "}\n",
       "\n",
       "\n",
       "\\newcommand\\particle[2]{%\n",
       "  \\begin{tikzpicture}[x=2cm, y=2cm]\n",
       "  \n",
       "\n",
       "  % Calculate the ratio of nucleus to cytosol concentration\n",
       "  \\def\\nratio{\\fpeval{ round(#1/(#1 + #2),2)}  };\n",
       "  \\def\\cratio{\\fpeval{ round(#2/(#1 + #2),2)}  };\n",
       "\n",
       "  \\def\\nconc{\\fpeval{ round(#1,1)}  };\n",
       "  \\def\\cconc{\\fpeval{ round(#2,1)}  };\n",
       "  \n",
       "  %Node for Circles\n",
       "  \\node at (0,0) [circle,draw, scale=1 ,fill=green!\\fpeval{round(100*(\\cratio))}!gray] (c2) {};\n",
       "  \n",
       "  \\node at (0,0) [circle,draw, scale=0.5 ,fill=green!\\fpeval{round(100*(\\nratio))}!gray] (c1) {};\n",
       "  \n",
       "  \n",
       "  %Node for line ends\n",
       "  \\node [inner sep=0,outer sep=0, xshift=0.2cm] at (c1.east) (n_conc) {};\n",
       "  \\node [inner sep=0,outer sep=0,yshift = -0.09cm] at (n_conc.south) (c_conc) {};\n",
       "  \n",
       "  % Node for data\n",
       "  \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (n_conc.east) {\\scalebox{.2}{\\nconc} };\n",
       "  \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (c_conc.east) {\\scalebox{.2}{\\cconc}};\n",
       "  \n",
       "  % Draw Lines\n",
       "  \\draw[-, very thin] (n_conc) -- (c1);\n",
       "  \\draw[-, very thin] (c_conc) -- (0.16cm,-0.1065cm);\n",
       "  \n",
       "  \\end{tikzpicture}\n",
       "}\n",
       "\n",
       "\\newcommand\\cell[2]{\n",
       "    \\begin{tikzpicture}[baseline={(c_conc.base)}, x=2cm, y=2cm, , outer sep=0]\n",
       "  \n",
       "        %Node for Circles\n",
       "        \\node at (0,0) [circle,draw, scale=1] (c2) {};\n",
       "        \n",
       "        \\node at (0,0) [circle,draw, scale=0.5] (c1) {};\n",
       "        \n",
       "        \n",
       "        %Node for line ends\n",
       "        \\node [inner sep=0,outer sep=0, xshift=0.2cm] at (c1.east) (n_conc) {};\n",
       "        \\node [inner sep=0,outer sep=0,yshift = -0.09cm] at (n_conc.south) (c_conc) {};\n",
       "        \n",
       "        % Node for data\n",
       "        \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (n_conc.east) {\\scalebox{.2}{#1} };\n",
       "        \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (c_conc.east) {\\scalebox{.2}{#2}};\n",
       "        \n",
       "        % Draw Lines\n",
       "        \\draw[-, very thin] (n_conc) -- (c1);\n",
       "        \\draw[-, very thin] (c_conc) -- (0.16cm,-0.1065cm);\n",
       "        \\end{tikzpicture}\n",
       "    \n",
       "}\n",
       "\n",
       "\\newcommand\\drawcell[2]{%\n",
       "    \\begin{tikzpicture}[baseline={(c_conc.base)}, outer sep=0]\n",
       "        \\def\\sc{3}\n",
       "        \\node at (0,0) [scale=\\sc] {\\cell{#1}{#2}};\n",
       "    \\end{tikzpicture}\n",
       "}\n",
       "\n",
       "\\newcommand\\drawRatio[2]{%\n",
       "    \\begin{tikzpicture}[baseline={(c_conc.base)}, outer sep=0]\n",
       "        \\def\\sc{3}\n",
       "        \\node at (0,0) [scale=\\sc] {\\particle{#1}{#2}};\n",
       "    \\end{tikzpicture}\n",
       "}\n",
       "\n",
       "\n",
       "\n",
       "\\begin{document}\n",
       "\n",
       "\\begin{tabular}[c]{p{1.4cm}p{1.8cm}p{2.8cm}|p{1.8cm}p{1.6cm}}\n",
       "    \\toprule\n",
       "    \\multicolumn{1}{c}{} & \\multicolumn{2}{c}{\\textbf{Healthy Mitochondria}} & \\multicolumn{2}{c}{\\textbf{Damaged Mitochondria}} \\\\ \\midrule\n",
       "     &\\textbf{Simulation} & \\multicolumn{1}{c}{\\textbf{Data}}\\hspace{0.52cm}  & \\textbf{Simulation} & \\hspace{0.5cm}\\textbf{Data}  \\\\ \n",
       "     &   \\multicolumn{4}{c}{\\textbf{Rtg3-GFP}}  \\\\\n",
       "    WT & \\drawRatio{215.7662572994662}{193.73735468865948} & \\drawRatio{0}{1} & \\drawRatio{346.2757699180584}{63.22784207023777} & \\drawRatio{1}{0} \\\\\n",
       "    \\Del{Rtg1} & \\drawRatio{366.1582049113594}{43.34580707693283} & \\drawRatio{1}{0}  & \\drawRatio{366.1589600110554}{43.34505197723719} & \\drawRatio{1}{0} \\\\\n",
       "    \\Del{Rtg2} & \\drawRatio{215.76640011596893}{193.737211869589} & \\drawRatio{0}{1}& \\drawRatio{215.76640470566127}{193.73720728246383} & \\drawRatio{0}{1} \\\\\n",
       "    \\Del{Mks} & \\drawRatio{347.64927120440973}{61.85434078386726} & \\drawRatio{1}{0}& \\multicolumn{2}{r}{}  \\\\\n",
       "    \\Del{Rtg2}\\Del{Mks} & \\drawRatio{347.64927315432374}{43.34580707693283} & \\drawRatio{1}{0} & \\multicolumn{2}{r}{} \\\\ \n",
       "     &   \\multicolumn{4}{c}{\\textbf{Rtg1-GFP}}   \\\\\n",
       "    WT & \\drawRatio{54.89009874232648}{91.03025761443399} & \\drawRatio{0}{1} & \\drawRatio{110.37166243874616}{35.54869391809153} & \\drawRatio{1}{0} \\\\\n",
       "    \\Del{Rtg3} & \\drawRatio{0.07820900778318428}{145.842547349088} & \\drawRatio{0}{1}& \\drawRatio{0.07845351771792033}{145.84230283909895} & \\drawRatio{0}{1} \\\\\n",
       "    \\Del{Rtg2} & \\drawRatio{54.890193652195336}{91.03016269915003} & \\drawRatio{0}{1} & \\drawRatio{54.89019658629695}{91.0301597704889} & \\drawRatio{0}{1} \\\\ \n",
       "    \\Del{Mks} & \\drawRatio{111.06393160920344}{34.856424747619194} & \\drawRatio{1}{0}& \\multicolumn{2}{r}{}  \\\\\n",
       "    \\Del{Rtg2}\\Del{Mks} & \\drawRatio{111.06393280959674}{34.856423547230804} & \\drawRatio{1}{0} & \\multicolumn{2}{r}{} \\\\ \n",
       "      &   \\multicolumn{4}{c}{\\textbf{Rtg2-GFP}}   \\\\\n",
       "    WT & \\drawRatio{0}{651.6543766184084} & \\drawRatio{0}{1} & \\drawRatio{0}{651.6543766184084} & \\drawRatio{0}{1} \\\\\n",
       "    &  \\multicolumn{4}{c}{\n",
       "        \n",
       "    \\begin{tikzpicture}\n",
       "        \\node [] (cell) {\\drawcell{Nucleus}{Cytosol}};\n",
       "        \\node [ right of=cell, xshift=1.5cm] (col) {\\colorBar};\n",
       "    \\end{tikzpicture}\n",
       "    } \n",
       "    \n",
       "    \\\\\n",
       "    \\bottomrule\n",
       "\\end{tabular}\n",
       "\n",
       "\\end{document}\n"
      ],
      "text/plain": [
       "L\"\\documentclass[border={5pt 0pt 20pt 5pt}, preview]{standalone}\n",
       "\n",
       "\\usepackage{pgfplots}\n",
       "\\pgfplotsset{compat=1.15}\n",
       "\\usepackage{xcolor}\n",
       "\n",
       "\n",
       "\\usepackage{tikz}\n",
       "\\usepackage[utf8]{inputenc}\n",
       "\\usepackage{xfp}\n",
       "\\usepackage{booktabs}\n",
       "\\usetikzlibrary{calc}\n",
       "\\usepackage{graphicx}\n",
       "\n",
       "\\newcommand{\\Del}[1]{\\textit{$\\Delta$\\MakeLowercase{#1}}}\n",
       "\\newcommand\\ratio[2]{%\n",
       "    \\pgfmathparse{ #1/(#1 + #2)}\\pgfmathresult\n",
       "}\n",
       "\n",
       "\n",
       "\\newcommand\\colorBar{\n",
       "    \\begin{tikzpicture}[baseline={(0,0)}, inner sep=0,outer sep=0]\n",
       "\n",
       "       \n",
       "        \\pgfdeclarehorizontalshading{someShading}{4cm}{\n",
       "        color(0cm)=(green!0!gray);\n",
       "        color(4cm)=(green!100!gray)\n",
       "        }\n",
       "        \n",
       "        \\shade [shading=someShading, yshift=-1cm]  (0,0) rectangle ++(1,0.3);\n",
       "        \\node [] at (0,-1.3) {0};\n",
       "        \\node [] at (1,-1.3) {1};\n",
       "        \n",
       "        \\end{tikzpicture}\n",
       "}\n",
       "\n",
       "\n",
       "\\newcommand\\particle[2]{%\n",
       "  \\begin{tikzpicture}[x=2cm, y=2cm]\n",
       "  \n",
       "\n",
       "  % Calculate the ratio of nucleus to cytosol concentration\n",
       "  \\def\\nratio{\\fpeval{ round(#1/(#1 + #2),2)}  };\n",
       "  \\def\\cratio{\\fpeval{ round(#2/(#1 + #2),2)}  };\n",
       "\n",
       "  \\def\\nconc{\\fpeval{ round(#1,1)}  };\n",
       "  \\def\\cconc{\\fpeval{ round(#2,1)}  };\n",
       "  \n",
       "  %Node for Circles\n",
       "  \\node at (0,0) [circle,draw, scale=1 ,fill=green!\\fpeval{round(100*(\\cratio))}!gray] (c2) {};\n",
       "  \n",
       "  \\node at (0,0) [circle,draw, scale=0.5 ,fill=green!\\fpeval{round(100*(\\nratio))}!gray] (c1) {};\n",
       "  \n",
       "  \n",
       "  %Node for line ends\n",
       "  \\node [inner sep=0,outer sep=0, xshift=0.2cm] at (c1.east) (n_conc) {};\n",
       "  \\node [inner sep=0,outer sep=0,yshift = -0.09cm] at (n_conc.south) (c_conc) {};\n",
       "  \n",
       "  % Node for data\n",
       "  \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (n_conc.east) {\\scalebox{.2}{\\nconc} };\n",
       "  \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (c_conc.east) {\\scalebox{.2}{\\cconc}};\n",
       "  \n",
       "  % Draw Lines\n",
       "  \\draw[-, very thin] (n_conc) -- (c1);\n",
       "  \\draw[-, very thin] (c_conc) -- (0.16cm,-0.1065cm);\n",
       "  \n",
       "  \\end{tikzpicture}\n",
       "}\n",
       "\n",
       "\\newcommand\\cell[2]{\n",
       "    \\begin{tikzpicture}[baseline={(c_conc.base)}, x=2cm, y=2cm, , outer sep=0]\n",
       "  \n",
       "        %Node for Circles\n",
       "        \\node at (0,0) [circle,draw, scale=1] (c2) {};\n",
       "        \n",
       "        \\node at (0,0) [circle,draw, scale=0.5] (c1) {};\n",
       "        \n",
       "        \n",
       "        %Node for line ends\n",
       "        \\node [inner sep=0,outer sep=0, xshift=0.2cm] at (c1.east) (n_conc) {};\n",
       "        \\node [inner sep=0,outer sep=0,yshift = -0.09cm] at (n_conc.south) (c_conc) {};\n",
       "        \n",
       "        % Node for data\n",
       "        \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (n_conc.east) {\\scalebox{.2}{#1} };\n",
       "        \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (c_conc.east) {\\scalebox{.2}{#2}};\n",
       "        \n",
       "        % Draw Lines\n",
       "        \\draw[-, very thin] (n_conc) -- (c1);\n",
       "        \\draw[-, very thin] (c_conc) -- (0.16cm,-0.1065cm);\n",
       "        \\end{tikzpicture}\n",
       "    \n",
       "}\n",
       "\n",
       "\\newcommand\\drawcell[2]{%\n",
       "    \\begin{tikzpicture}[baseline={(c_conc.base)}, outer sep=0]\n",
       "        \\def\\sc{3}\n",
       "        \\node at (0,0) [scale=\\sc] {\\cell{#1}{#2}};\n",
       "    \\end{tikzpicture}\n",
       "}\n",
       "\n",
       "\\newcommand\\drawRatio[2]{%\n",
       "    \\begin{tikzpicture}[baseline={(c_conc.base)}, outer sep=0]\n",
       "        \\def\\sc{3}\n",
       "        \\node at (0,0) [scale=\\sc] {\\particle{#1}{#2}};\n",
       "    \\end{tikzpicture}\n",
       "}\n",
       "\n",
       "\n",
       "\n",
       "\\begin{document}\n",
       "\n",
       "\\begin{tabular}[c]{p{1.4cm}p{1.8cm}p{2.8cm}|p{1.8cm}p{1.6cm}}\n",
       "    \\toprule\n",
       "    \\multicolumn{1}{c}{} & \\multicolumn{2}{c}{\\textbf{Healthy Mitochondria}} & \\multicolumn{2}{c}{\\textbf{Damaged Mitochondria}} \\\\ \\midrule\n",
       "     &\\textbf{Simulation} & \\multicolumn{1}{c}{\\textbf{Data}}\\hspace{0.52cm}  & \\textbf{Simulation} & \\hspace{0.5cm}\\textbf{Data}  \\\\ \n",
       "     &   \\multicolumn{4}{c}{\\textbf{Rtg3-GFP}}  \\\\\n",
       "    WT & \\drawRatio{215.7662572994662}{193.73735468865948} & \\drawRatio{0}{1} & \\drawRatio{346.2757699180584}{63.22784207023777} & \\drawRatio{1}{0} \\\\\n",
       "    \\Del{Rtg1} & \\drawRatio{366.1582049113594}{43.34580707693283} & \\drawRatio{1}{0}  & \\drawRatio{366.1589600110554}{43.34505197723719} & \\drawRatio{1}{0} \\\\\n",
       "    \\Del{Rtg2} & \\drawRatio{215.76640011596893}{193.737211869589} & \\drawRatio{0}{1}& \\drawRatio{215.76640470566127}{193.73720728246383} & \\drawRatio{0}{1} \\\\\n",
       "    \\Del{Mks} & \\drawRatio{347.64927120440973}{61.85434078386726} & \\drawRatio{1}{0}& \\multicolumn{2}{r}{}  \\\\\n",
       "    \\Del{Rtg2}\\Del{Mks} & \\drawRatio{347.64927315432374}{43.34580707693283} & \\drawRatio{1}{0} & \\multicolumn{2}{r}{} \\\\ \n",
       "     &   \\multicolumn{4}{c}{\\textbf{Rtg1-GFP}}   \\\\\n",
       "    WT & \\drawRatio{54.89009874232648}{91.03025761443399} & \\drawRatio{0}{1} & \\drawRatio{110.37166243874616}{35.54869391809153} & \\drawRatio{1}{0} \\\\\n",
       "    \\Del{Rtg3} & \\drawRatio{0.07820900778318428}{145.842547349088} & \\drawRatio{0}{1}& \\drawRatio{0.07845351771792033}{145.84230283909895} & \\drawRatio{0}{1} \\\\\n",
       "    \\Del{Rtg2} & \\drawRatio{54.890193652195336}{91.03016269915003} & \\drawRatio{0}{1} & \\drawRatio{54.89019658629695}{91.0301597704889} & \\drawRatio{0}{1} \\\\ \n",
       "    \\Del{Mks} & \\drawRatio{111.06393160920344}{34.856424747619194} & \\drawRatio{1}{0}& \\multicolumn{2}{r}{}  \\\\\n",
       "    \\Del{Rtg2}\\Del{Mks} & \\drawRatio{111.06393280959674}{34.856423547230804} & \\drawRatio{1}{0} & \\multicolumn{2}{r}{} \\\\ \n",
       "      &   \\multicolumn{4}{c}{\\textbf{Rtg2-GFP}}   \\\\\n",
       "    WT & \\drawRatio{0}{651.6543766184084} & \\drawRatio{0}{1} & \\drawRatio{0}{651.6543766184084} & \\drawRatio{0}{1} \\\\\n",
       "    &  \\multicolumn{4}{c}{\n",
       "        \n",
       "    \\begin{tikzpicture}\n",
       "        \\node [] (cell) {\\drawcell{Nucleus}{Cytosol}};\n",
       "        \\node [ right of=cell, xshift=1.5cm] (col) {\\colorBar};\n",
       "    \\end{tikzpicture}\n",
       "    } \n",
       "    \n",
       "    \\\\\n",
       "    \\bottomrule\n",
       "\\end{tabular}\n",
       "\n",
       "\\end{document}\n",
       "\""
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "TexPic = L\"\"\"\n",
    "\\documentclass[border={5pt 0pt 20pt 5pt}, preview]{standalone}\n",
    "\n",
    "\\usepackage{pgfplots}\n",
    "\\pgfplotsset{compat=1.15}\n",
    "\\usepackage{xcolor}\n",
    "\n",
    "\n",
    "\\usepackage{tikz}\n",
    "\\usepackage[utf8]{inputenc}\n",
    "\\usepackage{xfp}\n",
    "\\usepackage{booktabs}\n",
    "\\usetikzlibrary{calc}\n",
    "\\usepackage{graphicx}\n",
    "\n",
    "\\newcommand{\\Del}[1]{\\textit{$\\Delta$\\MakeLowercase{#1}}}\n",
    "\\newcommand\\ratio[2]{%\n",
    "    \\pgfmathparse{ #1/(#1 + #2)}\\pgfmathresult\n",
    "}\n",
    "\n",
    "\n",
    "\\newcommand\\colorBar{\n",
    "    \\begin{tikzpicture}[baseline={(0,0)}, inner sep=0,outer sep=0]\n",
    "\n",
    "       \n",
    "        \\pgfdeclarehorizontalshading{someShading}{4cm}{\n",
    "        color(0cm)=(green!0!gray);\n",
    "        color(4cm)=(green!100!gray)\n",
    "        }\n",
    "        \n",
    "        \\shade [shading=someShading, yshift=-1cm]  (0,0) rectangle ++(1,0.3);\n",
    "        \\node [] at (0,-1.3) {0};\n",
    "        \\node [] at (1,-1.3) {1};\n",
    "        \n",
    "        \\end{tikzpicture}\n",
    "}\n",
    "\n",
    "\n",
    "\\newcommand\\particle[2]{%\n",
    "  \\begin{tikzpicture}[x=2cm, y=2cm]\n",
    "  \n",
    "\n",
    "  % Calculate the ratio of nucleus to cytosol concentration\n",
    "  \\def\\nratio{\\fpeval{ round(#1/(#1 + #2),2)}  };\n",
    "  \\def\\cratio{\\fpeval{ round(#2/(#1 + #2),2)}  };\n",
    "\n",
    "  \\def\\nconc{\\fpeval{ round(#1,1)}  };\n",
    "  \\def\\cconc{\\fpeval{ round(#2,1)}  };\n",
    "  \n",
    "  %Node for Circles\n",
    "  \\node at (0,0) [circle,draw, scale=1 ,fill=green!\\fpeval{round(100*(\\cratio))}!gray] (c2) {};\n",
    "  \n",
    "  \\node at (0,0) [circle,draw, scale=0.5 ,fill=green!\\fpeval{round(100*(\\nratio))}!gray] (c1) {};\n",
    "  \n",
    "  \n",
    "  %Node for line ends\n",
    "  \\node [inner sep=0,outer sep=0, xshift=0.2cm] at (c1.east) (n_conc) {};\n",
    "  \\node [inner sep=0,outer sep=0,yshift = -0.09cm] at (n_conc.south) (c_conc) {};\n",
    "  \n",
    "  % Node for data\n",
    "  \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (n_conc.east) {\\scalebox{.2}{\\nconc} };\n",
    "  \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (c_conc.east) {\\scalebox{.2}{\\cconc}};\n",
    "  \n",
    "  % Draw Lines\n",
    "  \\draw[-, very thin] (n_conc) -- (c1);\n",
    "  \\draw[-, very thin] (c_conc) -- (0.16cm,-0.1065cm);\n",
    "  \n",
    "  \\end{tikzpicture}\n",
    "}\n",
    "\n",
    "\\newcommand\\cell[2]{\n",
    "    \\begin{tikzpicture}[baseline={(c_conc.base)}, x=2cm, y=2cm, , outer sep=0]\n",
    "  \n",
    "        %Node for Circles\n",
    "        \\node at (0,0) [circle,draw, scale=1] (c2) {};\n",
    "        \n",
    "        \\node at (0,0) [circle,draw, scale=0.5] (c1) {};\n",
    "        \n",
    "        \n",
    "        %Node for line ends\n",
    "        \\node [inner sep=0,outer sep=0, xshift=0.2cm] at (c1.east) (n_conc) {};\n",
    "        \\node [inner sep=0,outer sep=0,yshift = -0.09cm] at (n_conc.south) (c_conc) {};\n",
    "        \n",
    "        % Node for data\n",
    "        \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (n_conc.east) {\\scalebox{.2}{#1} };\n",
    "        \\node [inner sep=0,outer sep=0, xshift=0.cm, text width = 0cm, align=left] at (c_conc.east) {\\scalebox{.2}{#2}};\n",
    "        \n",
    "        % Draw Lines\n",
    "        \\draw[-, very thin] (n_conc) -- (c1);\n",
    "        \\draw[-, very thin] (c_conc) -- (0.16cm,-0.1065cm);\n",
    "        \\end{tikzpicture}\n",
    "    \n",
    "}\n",
    "\n",
    "\\newcommand\\drawcell[2]{%\n",
    "    \\begin{tikzpicture}[baseline={(c_conc.base)}, outer sep=0]\n",
    "        \\def\\sc{3}\n",
    "        \\node at (0,0) [scale=\\sc] {\\cell{#1}{#2}};\n",
    "    \\end{tikzpicture}\n",
    "}\n",
    "\n",
    "\\newcommand\\drawRatio[2]{%\n",
    "    \\begin{tikzpicture}[baseline={(c_conc.base)}, outer sep=0]\n",
    "        \\def\\sc{3}\n",
    "        \\node at (0,0) [scale=\\sc] {\\particle{#1}{#2}};\n",
    "    \\end{tikzpicture}\n",
    "}\n",
    "\n",
    "\n",
    "\n",
    "\\begin{document}\n",
    "\n",
    "\\begin{tabular}[c]{p{1.4cm}p{1.8cm}p{2.8cm}|p{1.8cm}p{1.6cm}}\n",
    "    \\toprule\n",
    "    \\multicolumn{1}{c}{} & \\multicolumn{2}{c}{\\textbf{Healthy Mitochondria}} & \\multicolumn{2}{c}{\\textbf{Damaged Mitochondria}} \\\\ \\midrule\n",
    "     &\\textbf{Simulation} & \\multicolumn{1}{c}{\\textbf{Data}}\\hspace{0.52cm}  & \\textbf{Simulation} & \\hspace{0.5cm}\\textbf{Data}  \\\\ \n",
    "     &   \\multicolumn{4}{c}{\\textbf{Rtg3-GFP}}  \\\\\n",
    "    WT & \\drawRatio{%$(transRes[\"nuc\"][7])}{%$(transRes[\"cyt\"][7])} & \\drawRatio{0}{1} & \\drawRatio{%$(transRes[\"nuc\"][8])}{%$(transRes[\"cyt\"][8])} & \\drawRatio{1}{0} \\\\\n",
    "    \\Del{Rtg1} & \\drawRatio{%$(transRes[\"nuc\"][3])}{%$(transRes[\"cyt\"][3])} & \\drawRatio{1}{0}  & \\drawRatio{%$(transRes[\"nuc\"][4])}{%$(transRes[\"cyt\"][4])} & \\drawRatio{1}{0} \\\\\n",
    "    \\Del{Rtg2} & \\drawRatio{%$(transRes[\"nuc\"][5])}{%$(transRes[\"cyt\"][5])} & \\drawRatio{0}{1}& \\drawRatio{%$(transRes[\"nuc\"][6])}{%$(transRes[\"cyt\"][6])} & \\drawRatio{0}{1} \\\\\n",
    "    \\Del{Mks} & \\drawRatio{%$(transRes[\"nuc\"][18])}{%$(transRes[\"cyt\"][18])} & \\drawRatio{1}{0}& \\multicolumn{2}{r}{}  \\\\\n",
    "    \\Del{Rtg2}\\Del{Mks} & \\drawRatio{%$(transRes[\"nuc\"][17])}{%$(transRes[\"cyt\"][3])} & \\drawRatio{1}{0} & \\multicolumn{2}{r}{} \\\\ \n",
    "     &   \\multicolumn{4}{c}{\\textbf{Rtg1-GFP}}   \\\\\n",
    "    WT & \\drawRatio{%$(transRes[\"nuc\"][15])}{%$(transRes[\"cyt\"][15])} & \\drawRatio{0}{1} & \\drawRatio{%$(transRes[\"nuc\"][16])}{%$(transRes[\"cyt\"][16])} & \\drawRatio{1}{0} \\\\\n",
    "    \\Del{Rtg3} & \\drawRatio{%$(transRes[\"nuc\"][11])}{%$(transRes[\"cyt\"][11])} & \\drawRatio{0}{1}& \\drawRatio{%$(transRes[\"nuc\"][12])}{%$(transRes[\"cyt\"][12])} & \\drawRatio{0}{1} \\\\\n",
    "    \\Del{Rtg2} & \\drawRatio{%$(transRes[\"nuc\"][13])}{%$(transRes[\"cyt\"][13])} & \\drawRatio{0}{1} & \\drawRatio{%$(transRes[\"nuc\"][14])}{%$(transRes[\"cyt\"][14])} & \\drawRatio{0}{1} \\\\ \n",
    "    \\Del{Mks} & \\drawRatio{%$(transRes[\"nuc\"][20])}{%$(transRes[\"cyt\"][20])} & \\drawRatio{1}{0}& \\multicolumn{2}{r}{}  \\\\\n",
    "    \\Del{Rtg2}\\Del{Mks} & \\drawRatio{%$(transRes[\"nuc\"][19])}{%$(transRes[\"cyt\"][19])} & \\drawRatio{1}{0} & \\multicolumn{2}{r}{} \\\\ \n",
    "      &   \\multicolumn{4}{c}{\\textbf{Rtg2-GFP}}   \\\\\n",
    "    WT & \\drawRatio{0}{%$Rtg2} & \\drawRatio{0}{1} & \\drawRatio{0}{%$Rtg2} & \\drawRatio{0}{1} \\\\\n",
    "    &  \\multicolumn{4}{c}{\n",
    "        \n",
    "    \\begin{tikzpicture}\n",
    "        \\node [] (cell) {\\drawcell{Nucleus}{Cytosol}};\n",
    "        \\node [ right of=cell, xshift=1.5cm] (col) {\\colorBar};\n",
    "    \\end{tikzpicture}\n",
    "    } \n",
    "    \n",
    "    \\\\\n",
    "    \\bottomrule\n",
    "\\end{tabular}\n",
    "\n",
    "\\end{document}\n",
    "\"\"\"\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5536"
      ]
     },
     "execution_count": 45,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "open(\"SteadyStates/result/verification/PLOT_SteadyStateVerification.tex\", \"w\") do io\n",
    "           write(io, TexPic)\n",
    "       end"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# ;cd SteadyStates/result/verification/ "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "This is XeTeX, Version 3.14159265-2.6-0.99998 (TeX Live 2017/Debian) (preloaded format=xelatex)\n",
      " restricted \\write18 enabled.\n",
      "entering extended mode\n",
      "! I can't find file `PLOT_SteadyStateVerification'.\n",
      "<*> PLOT_SteadyStateVerification \n",
      "                                 -synctex=1\n",
      "(Press Enter to retry, or Control-D to exit)\n",
      "Please type another input file name: \n",
      "! Emergency stop.\n",
      "<*> PLOT_SteadyStateVerification \n",
      "                                 -synctex=1\n",
      "No pages of output.\n",
      "Transcript written on texput.log.\n"
     ]
    }
   ],
   "source": [
    ";xelatex PLOT_SteadyStateVerification  -synctex=1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/ubuntu\n"
     ]
    }
   ],
   "source": [
    ";cd ../../../"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/ubuntu\n"
     ]
    }
   ],
   "source": [
    ";pwd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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  "language_info": {
   "file_extension": ".jl",
   "mimetype": "application/julia",
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