Interpretation-SC.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "b048062e",
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import torch\n",
    "from torch.utils.data import DataLoader\n",
    "\n",
    "from classifier import ProCNN, Tensorize, Vocab\n",
    "from data import PandasDataset\n",
    "from interpretation_utilities import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "777f3eb4",
   "metadata": {},
   "outputs": [],
   "source": [
    "USE_CUDA = True"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2c128188",
   "metadata": {},
   "source": [
    "## Model Hyperparameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "e4587cde",
   "metadata": {},
   "outputs": [],
   "source": [
    "CONFIG = {\n",
    "   \"learning_rate\": 0.00010229218879330196,\n",
    "   \"weight_decay\": 0.0016447149582678627,\n",
    "   \"xt_hidden\": 1024,\n",
    "   \"seq_length\": 1000,\n",
    "   \"conv1_ksize\": 9,\n",
    "   \"conv1_knum\": 256,\n",
    "   \"pool1\": 19,\n",
    "   \"conv2_ksize\": 13,\n",
    "   \"conv2_knum\": 64,\n",
    "   \"pool2\": 8,\n",
    "   \"batch_size\": 256,\n",
    "   \"conv_activation\" : \"relu\",\n",
    "   \"fc_activation\" : \"elu\",\n",
    "   \"conv_dropout\": 0.3981796388676127,\n",
    "   \"tf_dropout\": 0.18859739941162465,\n",
    "   \"fc_dropout\": 0.016570328292903613,\n",
    "   \"use_cuda\": USE_CUDA,\n",
    "   \"prefix\":'sc_elem_',\n",
    "   \"num_tfs\":208\n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "786945ea",
   "metadata": {},
   "source": [
    "## Device Setup"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "7673e637",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "using gpu\n"
     ]
    }
   ],
   "source": [
    "if USE_CUDA:\n",
    "    print(\"using gpu\")\n",
    "    cuda = torch.device('cuda')\n",
    "    FloatTensor = torch.cuda.FloatTensor\n",
    "    LongTensor = torch.cuda.LongTensor\n",
    "    def cudaify(model):\n",
    "        return model.cuda()\n",
    "else: \n",
    "    print(\"using cpu\")\n",
    "    cuda = torch.device('cpu')\n",
    "    FloatTensor = torch.FloatTensor\n",
    "    LongTensor = torch.LongTensor\n",
    "    def cudaify(model):\n",
    "        return model"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1d4c9de9",
   "metadata": {},
   "source": [
    "## Load Data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "609ad34d",
   "metadata": {},
   "outputs": [],
   "source": [
    "dataset = PandasDataset('/home/simonl2/yeast/Gene_Expression_Pred/Dec_Jan_Runs/Data_pkl/sc_file_oav_filt05_filtcv3_Zlog_new_allUniqueGenes_fixedTF.pkl')\n",
    "loader = DataLoader(dataset, batch_size=64, num_workers=8, pin_memory=True, shuffle=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "546a0308",
   "metadata": {},
   "outputs": [],
   "source": [
    "char_vocab = Vocab(['A', 'C', 'G', 'N', 'T'])    \n",
    "tens = Tensorize(char_vocab, CONFIG[\"seq_length\"], cudaify)\n",
    "char_vocab.index_map\n",
    "char_vocab_inv_map = {v: k for k, v in char_vocab.index_map.items()}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "27a66743",
   "metadata": {},
   "outputs": [],
   "source": [
    "def extract_nucleotide_alphabet(dataset):\n",
    "    symbols = set()\n",
    "    all_symbols = []\n",
    "    for sequence in dataset.select('seq'):\n",
    "        letters = set(sequence)\n",
    "        symbols = symbols | letters\n",
    "        all_symbols += list(sequence)\n",
    "        \n",
    "    freqs = dict()\n",
    "    for sym in symbols:\n",
    "        freqs[sym] = sum([1 for i in all_symbols if i == sym]) / len(all_symbols)\n",
    "        \n",
    "    return sorted(list(symbols)), freqs\n",
    "\n",
    "_, frequencies = extract_nucleotide_alphabet(dataset)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a382b08e",
   "metadata": {},
   "source": [
    "## Load Model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "053e35fb",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ProCNN(\n",
       "  (conv1): Conv1d(5, 256, kernel_size=(9,), stride=(1,), padding=(4,))\n",
       "  (pool1): MaxPool1d(kernel_size=19, stride=19, padding=0, dilation=1, ceil_mode=False)\n",
       "  (activation1): ReLU()\n",
       "  (conv1dropout): Dropout(p=0.3981796388676127, inplace=False)\n",
       "  (conv1bn): BatchNorm1d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n",
       "  (conv2): Conv1d(256, 64, kernel_size=(13,), stride=(1,), padding=(6,))\n",
       "  (pool2): MaxPool1d(kernel_size=8, stride=8, padding=0, dilation=1, ceil_mode=False)\n",
       "  (activation2): ReLU()\n",
       "  (conv2dropout): Dropout(p=0.3981796388676127, inplace=False)\n",
       "  (conv2bn): BatchNorm1d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n",
       "  (fc_t): Linear(in_features=208, out_features=1024, bias=True)\n",
       "  (fc_t_activation): ELU(alpha=1.0)\n",
       "  (fc_t_dropout): Dropout(p=0.016570328292903613, inplace=False)\n",
       "  (fc1): Linear(in_features=1408, out_features=512, bias=True)\n",
       "  (fc1_activation): ELU(alpha=1.0)\n",
       "  (fc1_dropout): Dropout(p=0.016570328292903613, inplace=False)\n",
       "  (bn1): BatchNorm1d(512, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n",
       "  (fc2): Linear(in_features=512, out_features=256, bias=True)\n",
       "  (fc2_activation): ELU(alpha=1.0)\n",
       "  (fc2_dropout): Dropout(p=0.016570328292903613, inplace=False)\n",
       "  (bn2): BatchNorm1d(256, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n",
       "  (fc3): Linear(in_features=256, out_features=64, bias=True)\n",
       "  (fc3_activation): ELU(alpha=1.0)\n",
       "  (fc3_dropout): Dropout(p=0.016570328292903613, inplace=False)\n",
       "  (bn3): BatchNorm1d(64, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)\n",
       "  (fc_out): Linear(in_features=64, out_features=1, bias=True)\n",
       ")"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "checkpoint_state = torch.load('/home/simonl2/yeast/Gene_Expression_Pred/Dec_Jan_Runs/sc_elem_best_net/checkpoint.pt')\n",
    "model = ProCNN(CONFIG, 1, char_vocab)\n",
    "model.load_state_dict(checkpoint_state[\"model_state_dict\"])\n",
    "model.eval()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "51e14b89",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Sequential(\n",
       "  (0): Conv1d(5, 256, kernel_size=(9,), stride=(1,), padding=(4,))\n",
       "  (1): ReLU()\n",
       ")"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cnn_conv = torch.nn.Sequential(*list(model.children())[:1]+[torch.nn.ReLU()])\n",
    "cnn_conv = cudaify(cnn_conv)\n",
    "cnn_conv"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d4cd8dd4",
   "metadata": {},
   "source": [
    "## Generate Feature Maps"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "5b378790",
   "metadata": {},
   "outputs": [],
   "source": [
    "cnn_conv.eval()\n",
    "fmap = []\n",
    "x_test = []\n",
    "with torch.no_grad():\n",
    "    for i, data in enumerate(loader):\n",
    "        input_s, _, _ = tens(data)\n",
    "        fmap.append(cnn_conv(input_s).to(\"cpu\"))\n",
    "        x_test.append(input_s.to(\"cpu\"))\n",
    "            \n",
    "fmap = np.concatenate(fmap)\n",
    "x_test = np.concatenate(x_test)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "6f6efe5a",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(2101, 256, 1000) (2101, 5, 1000)\n"
     ]
    }
   ],
   "source": [
    "print(fmap.shape, x_test.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "92098e29",
   "metadata": {},
   "outputs": [],
   "source": [
    "torch.save(fmap, f\"sc-elem-promoters-fmap.pt\", pickle_protocol=4)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8a5dedf3",
   "metadata": {},
   "source": [
    "## Generate PWMs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "92ccb454",
   "metadata": {},
   "outputs": [],
   "source": [
    "window = 9\n",
    "c = 1\n",
    "percentile_cutoff = 99.5\n",
    "top_k = fmap.shape[0] * 5 # Top 0.5% of each filter\n",
    "\n",
    "promoter_pwms, promoter_entropies = get_pwms(x_test, fmap, window, c, top_k)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "16b72cc8",
   "metadata": {},
   "outputs": [],
   "source": [
    "torch.save(promoter_pwms, f\"sc-elem-promoters-window{window}-top{top_k}-pwms.pt\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "9528801e",
   "metadata": {},
   "outputs": [],
   "source": [
    "prefix = f\"sc-elem-promoters-window{window}-top{top_k}\"\n",
    "\n",
    "meme_string = get_MEME_string(promoter_pwms, frequencies, window)\n",
    "with open(f\"{prefix}-filter_pwm.txt\", \"w\") as f:\n",
    "    f.write(meme_string)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "59a902c1",
   "metadata": {},
   "source": [
    "## Generate Motif Figures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "557f6611",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n",
      " Warning: Character 'N' is not in color_dict. Using black.\n"
     ]
    },
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m/tmp/ipykernel_545249/731959625.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      8\u001b[0m         \u001b[0mend\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpage\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m*\u001b[0m \u001b[0mNUM_PER_PAGE\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpromoter_pwms\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      9\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 10\u001b[0;31m         filter_plots = plot_promoter_filters(\n\u001b[0m\u001b[1;32m     11\u001b[0m             \u001b[0mpromoter_pwms\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     12\u001b[0m             \u001b[0mfmap\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/yeast/model-code/FUN-PROSE/interpretation_utilities.py\u001b[0m in \u001b[0;36mplot_promoter_filters\u001b[0;34m(filters, feature_maps, percentile_cutoff, selection, entropies)\u001b[0m\n\u001b[1;32m    214\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    215\u001b[0m         \u001b[0;31m# Also do a zero filter\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 216\u001b[0;31m         \u001b[0mtransformed_fmap\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mtransformed_fmap\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnan\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    217\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    218\u001b[0m         \u001b[0mfeature_length\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfeature_maps\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Error in callback <function flush_figures at 0x7ffe66d4e8b0> (for post_execute):\n"
     ]
    },
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib_inline/backend_inline.py\u001b[0m in \u001b[0;36mflush_figures\u001b[0;34m()\u001b[0m\n\u001b[1;32m    119\u001b[0m         \u001b[0;31m# ignore the tracking, just draw and close all figures\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    120\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 121\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mshow\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    122\u001b[0m         \u001b[0;32mexcept\u001b[0m \u001b[0mException\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    123\u001b[0m             \u001b[0;31m# safely show traceback if in IPython, else raise\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib_inline/backend_inline.py\u001b[0m in \u001b[0;36mshow\u001b[0;34m(close, block)\u001b[0m\n\u001b[1;32m     39\u001b[0m     \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     40\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mfigure_manager\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mGcf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_all_fig_managers\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 41\u001b[0;31m             display(\n\u001b[0m\u001b[1;32m     42\u001b[0m                 \u001b[0mfigure_manager\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcanvas\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfigure\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     43\u001b[0m                 \u001b[0mmetadata\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0m_fetch_figure_metadata\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfigure_manager\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcanvas\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfigure\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/IPython/core/display.py\u001b[0m in \u001b[0;36mdisplay\u001b[0;34m(include, exclude, metadata, transient, display_id, *objs, **kwargs)\u001b[0m\n\u001b[1;32m    318\u001b[0m             \u001b[0mpublish_display_data\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmetadata\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmetadata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    319\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 320\u001b[0;31m             \u001b[0mformat_dict\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmd_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minclude\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0minclude\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mexclude\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mexclude\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    321\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mformat_dict\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    322\u001b[0m                 \u001b[0;31m# nothing to display (e.g. _ipython_display_ took over)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/IPython/core/formatters.py\u001b[0m in \u001b[0;36mformat\u001b[0;34m(self, obj, include, exclude)\u001b[0m\n\u001b[1;32m    178\u001b[0m             \u001b[0mmd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    179\u001b[0m             \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 180\u001b[0;31m                 \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mformatter\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    181\u001b[0m             \u001b[0;32mexcept\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    182\u001b[0m                 \u001b[0;31m# FIXME: log the exception\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/decorator.py\u001b[0m in \u001b[0;36mfun\u001b[0;34m(*args, **kw)\u001b[0m\n\u001b[1;32m    230\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mkwsyntax\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    231\u001b[0m                 \u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkw\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfix\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkw\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 232\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mcaller\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfunc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mextras\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    233\u001b[0m     \u001b[0mfun\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__name__\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__name__\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    234\u001b[0m     \u001b[0mfun\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__doc__\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__doc__\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/IPython/core/formatters.py\u001b[0m in \u001b[0;36mcatch_format_error\u001b[0;34m(method, self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    222\u001b[0m     \u001b[0;34m\"\"\"show traceback on failed format call\"\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    223\u001b[0m     \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 224\u001b[0;31m         \u001b[0mr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmethod\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    225\u001b[0m     \u001b[0;32mexcept\u001b[0m \u001b[0mNotImplementedError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    226\u001b[0m         \u001b[0;31m# don't warn on NotImplementedErrors\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/IPython/core/formatters.py\u001b[0m in \u001b[0;36m__call__\u001b[0;34m(self, obj)\u001b[0m\n\u001b[1;32m    339\u001b[0m                 \u001b[0;32mpass\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    340\u001b[0m             \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 341\u001b[0;31m                 \u001b[0;32mreturn\u001b[0m \u001b[0mprinter\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    342\u001b[0m             \u001b[0;31m# Finally look for special method names\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    343\u001b[0m             \u001b[0mmethod\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mget_real_method\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprint_method\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/IPython/core/pylabtools.py\u001b[0m in \u001b[0;36mprint_figure\u001b[0;34m(fig, fmt, bbox_inches, base64, **kwargs)\u001b[0m\n\u001b[1;32m    149\u001b[0m         \u001b[0mFigureCanvasBase\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    150\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 151\u001b[0;31m     \u001b[0mfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcanvas\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprint_figure\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbytes_io\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    152\u001b[0m     \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mbytes_io\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgetvalue\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    153\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mfmt\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'svg'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/backend_bases.py\u001b[0m in \u001b[0;36mprint_figure\u001b[0;34m(self, filename, dpi, facecolor, edgecolor, orientation, format, bbox_inches, pad_inches, bbox_extra_artists, backend, **kwargs)\u001b[0m\n\u001b[1;32m   2228\u001b[0m                        else suppress())\n\u001b[1;32m   2229\u001b[0m                 \u001b[0;32mwith\u001b[0m \u001b[0mctx\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2230\u001b[0;31m                     \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfigure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdraw\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrenderer\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2231\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2232\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mbbox_inches\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/artist.py\u001b[0m in \u001b[0;36mdraw_wrapper\u001b[0;34m(artist, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m     72\u001b[0m     \u001b[0;34m@\u001b[0m\u001b[0mwraps\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdraw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     73\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mdraw_wrapper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0martist\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrenderer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 74\u001b[0;31m         \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdraw\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0martist\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrenderer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     75\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mrenderer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_rasterizing\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     76\u001b[0m             \u001b[0mrenderer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstop_rasterizing\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/artist.py\u001b[0m in \u001b[0;36mdraw_wrapper\u001b[0;34m(artist, renderer, *args, **kwargs)\u001b[0m\n\u001b[1;32m     49\u001b[0m                 \u001b[0mrenderer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstart_filter\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     50\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 51\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mdraw\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0martist\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrenderer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     52\u001b[0m         \u001b[0;32mfinally\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     53\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0martist\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_agg_filter\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/figure.py\u001b[0m in \u001b[0;36mdraw\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m   2779\u001b[0m             \u001b[0mrenderer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mopen_group\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'figure'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgid\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_gid\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2780\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_constrained_layout\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maxes\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2781\u001b[0;31m                 \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexecute_constrained_layout\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrenderer\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2782\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_tight_layout\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maxes\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2783\u001b[0m                 \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/figure.py\u001b[0m in \u001b[0;36mexecute_constrained_layout\u001b[0;34m(self, renderer)\u001b[0m\n\u001b[1;32m   3120\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mrenderer\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3121\u001b[0m             \u001b[0mrenderer\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mget_renderer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 3122\u001b[0;31m         \u001b[0mdo_constrained_layout\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfig\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrenderer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mh_pad\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mw_pad\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mhspace\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mwspace\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   3123\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3124\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mtight_layout\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpad\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1.08\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mh_pad\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mw_pad\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrect\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/_constrained_layout.py\u001b[0m in \u001b[0;36mdo_constrained_layout\u001b[0;34m(fig, renderer, h_pad, w_pad, hspace, wspace)\u001b[0m\n\u001b[1;32m    107\u001b[0m         \u001b[0;31m# make margins for all the axes and subfigures in the\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    108\u001b[0m         \u001b[0;31m# figure.  Add margins for colorbars...\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 109\u001b[0;31m         _make_layout_margins(fig, renderer, h_pad=h_pad, w_pad=w_pad,\n\u001b[0m\u001b[1;32m    110\u001b[0m                              hspace=hspace, wspace=wspace)\n\u001b[1;32m    111\u001b[0m         \u001b[0m_make_margin_suptitles\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfig\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrenderer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mh_pad\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mh_pad\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mw_pad\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mw_pad\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/_constrained_layout.py\u001b[0m in \u001b[0;36m_make_layout_margins\u001b[0;34m(fig, renderer, w_pad, h_pad, hspace, wspace)\u001b[0m\n\u001b[1;32m    222\u001b[0m                                            hspace=hspace, wspace=wspace)\n\u001b[1;32m    223\u001b[0m         \u001b[0mmargin0\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmargin\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcopy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 224\u001b[0;31m         \u001b[0mpos\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbbox\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_get_pos_and_bbox\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0max\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrenderer\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    225\u001b[0m         \u001b[0;31m# the margin is the distance between the bounding box of the axes\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    226\u001b[0m         \u001b[0;31m# and its position (plus the padding from above)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/_constrained_layout.py\u001b[0m in \u001b[0;36m_get_pos_and_bbox\u001b[0;34m(ax, renderer)\u001b[0m\n\u001b[1;32m    451\u001b[0m     \u001b[0mpos\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtransformed\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtransSubfigure\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0mfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtransFigure\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    452\u001b[0m     \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 453\u001b[0;31m         \u001b[0mtightbbox\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0max\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_tightbbox\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrenderer\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mrenderer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfor_layout_only\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    454\u001b[0m     \u001b[0;32mexcept\u001b[0m \u001b[0mTypeError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    455\u001b[0m         \u001b[0mtightbbox\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0max\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_tightbbox\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrenderer\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mrenderer\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/axes/_base.py\u001b[0m in \u001b[0;36mget_tightbbox\u001b[0;34m(self, renderer, call_axes_locator, bbox_extra_artists, for_layout_only)\u001b[0m\n\u001b[1;32m   4428\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mxaxis\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_visible\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   4429\u001b[0m                 \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 4430\u001b[0;31m                     bb_xaxis = self.xaxis.get_tightbbox(\n\u001b[0m\u001b[1;32m   4431\u001b[0m                         renderer, for_layout_only=for_layout_only)\n\u001b[1;32m   4432\u001b[0m                 \u001b[0;32mexcept\u001b[0m \u001b[0mTypeError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/axis.py\u001b[0m in \u001b[0;36mget_tightbbox\u001b[0;34m(self, renderer, for_layout_only)\u001b[0m\n\u001b[1;32m   1084\u001b[0m             \u001b[0;32mreturn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1085\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1086\u001b[0;31m         \u001b[0mticks_to_draw\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_update_ticks\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1087\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1088\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_update_label_position\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrenderer\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/axis.py\u001b[0m in \u001b[0;36m_update_ticks\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m   1028\u001b[0m         \u001b[0mmajor_locs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_majorticklocs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1029\u001b[0m         \u001b[0mmajor_labels\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmajor\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformatter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat_ticks\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmajor_locs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1030\u001b[0;31m         \u001b[0mmajor_ticks\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_major_ticks\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmajor_locs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1031\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmajor\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformatter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_locs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmajor_locs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1032\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mtick\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mloc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlabel\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mzip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmajor_ticks\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmajor_locs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmajor_labels\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/axis.py\u001b[0m in \u001b[0;36mget_major_ticks\u001b[0;34m(self, numticks)\u001b[0m\n\u001b[1;32m   1357\u001b[0m         \u001b[0;32mwhile\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmajorTicks\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m<\u001b[0m \u001b[0mnumticks\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1358\u001b[0m             \u001b[0;31m# Update the new tick label properties from the old.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1359\u001b[0;31m             \u001b[0mtick\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_tick\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmajor\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1360\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmajorTicks\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtick\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1361\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_copy_tick_props\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmajorTicks\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtick\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/axis.py\u001b[0m in \u001b[0;36m_get_tick\u001b[0;34m(self, major)\u001b[0m\n\u001b[1;32m   2057\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2058\u001b[0m             \u001b[0mtick_kw\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_minor_tick_kw\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2059\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mXTick\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maxes\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmajor\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmajor\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mtick_kw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2060\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2061\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mset_label_position\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mposition\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/axis.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    418\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    419\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 420\u001b[0;31m         \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    421\u001b[0m         \u001b[0;31m# x in data coords, y in axes coords\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    422\u001b[0m         self.tick1line.set(\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/_api/deprecation.py\u001b[0m in \u001b[0;36mwrapper\u001b[0;34m(*inner_args, **inner_kwargs)\u001b[0m\n\u001b[1;32m    429\u001b[0m                          \u001b[0;32melse\u001b[0m \u001b[0mdeprecation_addendum\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    430\u001b[0m                 **kwargs)\n\u001b[0;32m--> 431\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0minner_args\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0minner_kwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    432\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    433\u001b[0m     \u001b[0;32mreturn\u001b[0m \u001b[0mwrapper\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/axis.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, axes, loc, label, size, width, color, tickdir, pad, labelsize, labelcolor, zorder, gridOn, tick1On, tick2On, label1On, label2On, major, labelrotation, grid_color, grid_linestyle, grid_linewidth, grid_alpha, **kw)\u001b[0m\n\u001b[1;32m    172\u001b[0m             \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnan\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnan\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    173\u001b[0m             fontsize=labelsize, color=labelcolor, visible=label1On)\n\u001b[0;32m--> 174\u001b[0;31m         self.label2 = mtext.Text(\n\u001b[0m\u001b[1;32m    175\u001b[0m             \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnan\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnan\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    176\u001b[0m             fontsize=labelsize, color=labelcolor, visible=label2On)\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/text.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, x, y, text, color, verticalalignment, horizontalalignment, multialignment, fontproperties, rotation, linespacing, rotation_mode, usetex, wrap, transform_rotates_text, **kwargs)\u001b[0m\n\u001b[1;32m    169\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_linespacing\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlinespacing\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    170\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_rotation_mode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrotation_mode\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 171\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    172\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    173\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/text.py\u001b[0m in \u001b[0;36mupdate\u001b[0;34m(self, kwargs)\u001b[0m\n\u001b[1;32m    182\u001b[0m         \u001b[0;31m# Update bbox last, as it depends on font properties.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    183\u001b[0m         \u001b[0mbbox\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"bbox\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msentinel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 184\u001b[0;31m         \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    185\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mbbox\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0msentinel\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    186\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_bbox\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbbox\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/artist.py\u001b[0m in \u001b[0;36mupdate\u001b[0;34m(self, props)\u001b[0m\n\u001b[1;32m   1062\u001b[0m                         raise AttributeError(f\"{type(self).__name__!r} object \"\n\u001b[1;32m   1063\u001b[0m                                              f\"has no property {k!r}\")\n\u001b[0;32m-> 1064\u001b[0;31m                     \u001b[0mret\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mv\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1065\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mret\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1066\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpchanged\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/artist.py\u001b[0m in \u001b[0;36mset_visible\u001b[0;34m(self, b)\u001b[0m\n\u001b[1;32m   1001\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_visible\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mb\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1002\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpchanged\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1003\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstale\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1004\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1005\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mset_animated\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mb\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.conda/envs/yeast-raytune2/lib/python3.8/site-packages/matplotlib/artist.py\u001b[0m in \u001b[0;36mstale\u001b[0;34m(self, val)\u001b[0m\n\u001b[1;32m    239\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_stale\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    240\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 241\u001b[0;31m     \u001b[0;34m@\u001b[0m\u001b[0mstale\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msetter\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    242\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mstale\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mval\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    243\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_stale\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mval\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
     ]
    }
   ],
   "source": [
    "NUM_PER_PAGE = 16\n",
    "\n",
    "from matplotlib.backends.backend_pdf import PdfPages\n",
    "\n",
    "with PdfPages(f\"sc-elem-promoters-window{window}-smoothed-top{top_k}.pdf\") as pdf:\n",
    "    for page in range((len(promoter_pwms) + NUM_PER_PAGE - 1) // NUM_PER_PAGE):\n",
    "        start = page * NUM_PER_PAGE\n",
    "        end = min((page + 1) * NUM_PER_PAGE, len(promoter_pwms))\n",
    "        \n",
    "        filter_plots = plot_promoter_filters(\n",
    "            promoter_pwms, \n",
    "            fmap, \n",
    "            percentile_cutoff,\n",
    "            [*range(start, end)], \n",
    "            [promoter_entropies[i] for i in range(start, end)]\n",
    "        )\n",
    "        pdf.savefig(filter_plots)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "359e6ec6",
   "metadata": {},
   "source": [
    "## Motif Table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "25af6292",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "motifs_df = pd.DataFrame(\n",
    "    {\n",
    "        \"motif_id\": [i + 1 for i in range(len(promoter_pwms))],\n",
    "        f\"activation_{percentile_cutoff}\" : [activation_cutoff(fmap, i, percentile_cutoff) for i in range(len(promoter_pwms))],\n",
    "        \"entropy\": promoter_entropies,\n",
    "        \"uniform_chisquare\": [get_chisquare_uniform(fmap, i, percentile_cutoff) for i in range(len(promoter_pwms))],\n",
    "        \"consensus_sequence\": [get_consensus_sequence(promoter_pwms[i], char_vocab_inv_map) for i in range(len(promoter_pwms))],\n",
    "        \"top1pct_sequences\": [get_top_sequences(fmap, i, dataset, 99) for i in range(len(promoter_pwms))]\n",
    "    }\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "c85473c8",
   "metadata": {},
   "outputs": [],
   "source": [
    "motifs_df.to_csv(f\"sc-elem-promoters-window{window}-top{top_k}-motifs.tsv\", sep=\"\\t\", index=False)"
   ]
  }
 ],
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