notebooks/task_excel_to_latex_tables.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "23a9ed8f-5103-46b1-b55a-b61b8fad76a4",
   "metadata": {},
   "source": [
    "# Convert xlsx to latex\n",
    "In this notebook we convert the first sheet of the excel file in `gene_benchmark/tasks/task_descriptions.xlsx` to a set of latex tables, to allow easy insertion into the appendix of the related manuscript. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "48d050f6-9b66-49d8-8baa-ff258cae64a8",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "e8320f70-ff0c-47be-8655-1c11ea08f7b6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Task Name</th>\n",
       "      <th>Family</th>\n",
       "      <th>Type</th>\n",
       "      <th>Size</th>\n",
       "      <th>Description</th>\n",
       "      <th>Origin</th>\n",
       "      <th>Link</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Bivalent vs non-methylated</td>\n",
       "      <td>Genomic Properties</td>\n",
       "      <td>binary</td>\n",
       "      <td>133.0</td>\n",
       "      <td>Does the gene go through methylation or is it ...</td>\n",
       "      <td>GenePT</td>\n",
       "      <td>https://www.biorxiv.org/content/10.1101/2023.1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Chromosome</td>\n",
       "      <td>Genomic Properties</td>\n",
       "      <td>categorical</td>\n",
       "      <td>19784.0</td>\n",
       "      <td>Chromosome</td>\n",
       "      <td>human protein atlas</td>\n",
       "      <td>https://www.proteinatlas.org/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Dosage sensitive vs insensitive tf</td>\n",
       "      <td>Genomic Properties</td>\n",
       "      <td>binary</td>\n",
       "      <td>487.0</td>\n",
       "      <td>Is gene expression affected by the number of c...</td>\n",
       "      <td>GenePT</td>\n",
       "      <td>https://www.biorxiv.org/content/10.1101/2023.1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Lys4-only-methylated vs non-methylated</td>\n",
       "      <td>Genomic Properties</td>\n",
       "      <td>binary</td>\n",
       "      <td>171.0</td>\n",
       "      <td>Does gene go through Lys4 methylation</td>\n",
       "      <td>GenePT</td>\n",
       "      <td>http://humantfs.ccbr.utoronto.ca/download.php</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Protein class</td>\n",
       "      <td>Genomic Properties</td>\n",
       "      <td>multi label</td>\n",
       "      <td>19784.0</td>\n",
       "      <td>Protein class(es) of the gene product accordin...</td>\n",
       "      <td>human protein atlas</td>\n",
       "      <td>https://www.proteinatlas.org/</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                Task Name              Family          Type  \\\n",
       "0              Bivalent vs non-methylated  Genomic Properties        binary   \n",
       "1                              Chromosome  Genomic Properties  categorical    \n",
       "2      Dosage sensitive vs insensitive tf  Genomic Properties        binary   \n",
       "3  Lys4-only-methylated vs non-methylated  Genomic Properties        binary   \n",
       "4                           Protein class  Genomic Properties  multi label    \n",
       "\n",
       "      Size                                        Description  \\\n",
       "0    133.0  Does the gene go through methylation or is it ...   \n",
       "1  19784.0                                        Chromosome    \n",
       "2    487.0  Is gene expression affected by the number of c...   \n",
       "3    171.0              Does gene go through Lys4 methylation   \n",
       "4  19784.0  Protein class(es) of the gene product accordin...   \n",
       "\n",
       "                 Origin                                               Link  \n",
       "0                GenePT  https://www.biorxiv.org/content/10.1101/2023.1...  \n",
       "1  human protein atlas                       https://www.proteinatlas.org/  \n",
       "2                GenePT  https://www.biorxiv.org/content/10.1101/2023.1...  \n",
       "3                GenePT      http://humantfs.ccbr.utoronto.ca/download.php  \n",
       "4  human protein atlas                       https://www.proteinatlas.org/  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tasks = pd.read_excel(\"../gene_benchmark/tasks/task_descriptions.xlsx\")\n",
    "tasks.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "251d1be8-1cf3-47d2-afb3-848be74e7905",
   "metadata": {},
   "outputs": [],
   "source": [
    "# remove the NaN from size of Pathology prognostics to convert the column to int\n",
    "tasks.loc[49, \"Size\"] = 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "06fb2d59-3bc5-4057-a2b5-6d6e171ea478",
   "metadata": {},
   "outputs": [],
   "source": [
    "tasks[\"Size\"] = pd.to_numeric(tasks[\"Size\"], downcast=\"integer\")  # convert to integer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "3a14dac5-3def-4acf-8910-a236ac249e33",
   "metadata": {},
   "outputs": [],
   "source": [
    "def print_task_family_table(task_family: str, description: pd.DataFrame):\n",
    "    print(r\"\\begin{table}\")\n",
    "    print(\n",
    "        rf\"\\capation{{Detailed desctiption for the benchmarking tasks belonging to the family {task_family}}}\"\n",
    "    )\n",
    "    print(rf\"\\label{{tab:task_descriptions_{task_family.lower().replace(' ', '_')}}}\")\n",
    "    print(r\"\\centering\")\n",
    "    print(\n",
    "        description.to_latex(\n",
    "            columns=[\"Task Name\", \"Type\", \"Size\", \"Description\", \"Origin\"], index=False\n",
    "        )\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "20e6d6ae-6648-4b35-b630-01cf87553195",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\\begin{table}\n",
      "\\capation{Detailed desctiption for the benchmarking tasks belonging to the family Biological Processes}\n",
      "\\label{tab:task_descriptions_biological_processes}\n",
      "\\centering\n",
      "\\begin{tabular}{llrll}\n",
      "\\toprule\n",
      "Task Name & Type & Size & Description & Origin \\\\\n",
      "\\midrule\n",
      "Biological process & multi label  & 10796 & UniProt keywords indicating involvement in a particular biological process & human protein atlas  \\\\\n",
      "Ccd protein & binary & 1429 & Cell cycle dependent (CCD) proteins in the FUCCI U-2 OS cell line & human protein atlas  \\\\\n",
      "Ccd transcript & binary & 1631 & Cell cycle dependent (CCD) genes by RNA expression in the FUCCI u-2 OS cell line & human protein atlas  \\\\\n",
      "Disease involvement & multi label  & 5837 & UniProt keywords for disease, cancer, and FDA approved drug targets & human protein atlas  \\\\\n",
      "Gene-disease association & regression & 411569 & Disease-gene association score as derived from the open targets platform & open targets \\\\\n",
      "Hla class i vs class ii & binary & 44 & Identify class1 or class2 of the Histocompatibility complex (HLA)  & ScGPT\\HGNC \\\\\n",
      "Molecular function & multi label  & 10991 & Keywords assigned by UniProt to proteins due to their particular molecular function. & human protein atlas  \\\\\n",
      "Pathology prognostics & categorical  & 0 & Evidence level for being prognostic of survival in 17 cancer types (17 tasks) & human protein atlas  \\\\\n",
      "Pathways & multi label  & 10969 & Reactome top level pathways that include the gene (29 pathways) & reactome \\\\\n",
      "Rna cancer distribution & categorical  & 19588 & Classification of spatial distribution of gene by histochemistry & human protein atlas  \\\\\n",
      "Rna cancer specificity & categorical  & 19588 & Level of differential exppression compared to other tissues & human protein atlas  \\\\\n",
      "Rna cancer specificity score & regression & 2084 & Fold change between highest expression the second highest expression & human protein atlas  \\\\\n",
      "Secretome function & categorical  & 2736 & Functional annotation of involvement in cellular secretion & human protein atlas  \\\\\n",
      "Secretome location & categorical  & 2767 & The site of cellular secretion (if any) & human protein atlas  \\\\\n",
      "\\bottomrule\n",
      "\\end{tabular}\n",
      "\n",
      "\\begin{table}\n",
      "\\capation{Detailed desctiption for the benchmarking tasks belonging to the family Genomic Properties}\n",
      "\\label{tab:task_descriptions_genomic_properties}\n",
      "\\centering\n",
      "\\begin{tabular}{llrll}\n",
      "\\toprule\n",
      "Task Name & Type & Size & Description & Origin \\\\\n",
      "\\midrule\n",
      "Bivalent vs non-methylated & binary & 133 & Does the gene go through methylation or is it byvalant & GenePT \\\\\n",
      "Chromosome & categorical  & 19784 & Chromosome  & human protein atlas  \\\\\n",
      "Dosage sensitive vs insensitive tf & binary & 487 & Is gene expression affected by the number of copies it has & GenePT \\\\\n",
      "Lys4-only-methylated vs non-methylated & binary & 171 & Does gene go through Lys4 methylation & GenePT \\\\\n",
      "Protein class & multi label  & 19784 & Protein class(es) of the gene product according to selected gene lists & human protein atlas  \\\\\n",
      "Subcellular location & multi label  & 13039 & Sucellular Localization according to immunocytochemistry/IF & human protein atlas  \\\\\n",
      "\\bottomrule\n",
      "\\end{tabular}\n",
      "\n",
      "\\begin{table}\n",
      "\\capation{Detailed desctiption for the benchmarking tasks belonging to the family Localization}\n",
      "\\label{tab:task_descriptions_localization}\n",
      "\\centering\n",
      "\\begin{tabular}{llrll}\n",
      "\\toprule\n",
      "Task Name & Type & Size & Description & Origin \\\\\n",
      "\\midrule\n",
      "Blood concentration - conc. blood im & regression & 438 & Concentration of protein in blood stream & human protein atlas  \\\\\n",
      "Blood expression cluster (HPA) & categorical  & 12697 & Cluster assignment in blood-derived expression data & human protein atlas  \\\\\n",
      "Brain expression cluster (HPA) & categorical  & 17590 & Cluster assignment in brin-derived expression data & human protein atlas  \\\\\n",
      "Cell line expression cluster (HPA) & categorical  & 19167 & Cluster assignment in cell-line expression data & human protein atlas  \\\\\n",
      "Nextprot evidence & categorical  & 19179 & NeXtProt level of evidence supporting protein existence in tissue  & human protein atlas  \\\\\n",
      "Rna blood cell distribution & categorical  & 19784 & Classification of spatial distribution of gene by histochemistry & human protein atlas  \\\\\n",
      "Rna blood cell specificity & categorical  & 19784 & Level of differential exppression compared to other tissues & human protein atlas  \\\\\n",
      "Rna blood cell specificity score & regression & 2238 & Fold change between highest expression the second highest expression & human protein atlas  \\\\\n",
      "Rna blood lineage distribution & categorical  & 19784 & Classification of spatial distribution of gene by histochemistry & human protein atlas  \\\\\n",
      "Rna blood lineage specificity & categorical  & 19784 & Level of differential exppression compared to other tissues & human protein atlas  \\\\\n",
      "Rna blood lineage specificity score & regression & 3351 & Fold change between highest expression the second highest expression & human protein atlas  \\\\\n",
      "Rna brain regional distribution & categorical  & 19784 & Classification of spatial distribution of gene by histochemistry & human protein atlas  \\\\\n",
      "Rna brain regional specificity & categorical  & 19784 & Level of differential exppression compared to other tissues & human protein atlas  \\\\\n",
      "Rna brain regional specificity score & regression & 595 & Fold change between highest expression the second highest expression & human protein atlas  \\\\\n",
      "Rna cell line distribution & categorical  & 19784 & Classification of spatial distribution of gene by histochemistry & human protein atlas  \\\\\n",
      "Rna cell line specificity & categorical  & 19784 & Level of differential exppression compared to other tissues & human protein atlas  \\\\\n",
      "Rna cell line specificity score & regression & 2171 & Fold change between highest expression the second highest expression & human protein atlas  \\\\\n",
      "Rna mouse brain regional distribution & categorical  & 16655 & Classification of spatial distribution of gene by histochemistry & human protein atlas  \\\\\n",
      "Rna mouse brain regional specificity & categorical  & 16655 & Level of differential exppression compared to other tissues & human protein atlas  \\\\\n",
      "Rna pig brain regional distribution & categorical  & 16595 & Classification of spatial distribution of gene by histochemistry & human protein atlas  \\\\\n",
      "Rna pig brain regional specificity & categorical  & 16595 & Level of differential exppression compared to other tissues & human protein atlas  \\\\\n",
      "Rna single cell type distribution & categorical  & 19761 & Classification of spatial distribution of gene by histochemistry & human protein atlas  \\\\\n",
      "Rna single cell type specificity & categorical  & 19761 & Level of differential exppression compared to other tissues & human protein atlas  \\\\\n",
      "Rna single cell type specificity score & regression & 4798 & Fold change between highest expression the second highest expression & human protein atlas  \\\\\n",
      "Rna tissue cell type enrichment & multi label  & 13957 & The tissues in which the genes is significantly expressed & human protein atlas  \\\\\n",
      "Rna tissue distribution & categorical  & 19784 & Classification of spatial distribution of gene by histochemistry & human protein atlas  \\\\\n",
      "Rna tissue specificity & categorical  & 19784 & Level of differential exppression compared to other tissues & human protein atlas  \\\\\n",
      "Rna tissue specificity score & regression & 4653 & Fold change between highest expression the second highest expression & human protein atlas  \\\\\n",
      "Single cell expression cluster & categorical  & 19016 & Assignment to a cluster according to single-cell expression profile across tissues & human protein atlas  \\\\\n",
      "Tissue expression cluster & categorical  & 18355 & Assignment to a cluster according to bulk RNA expression profile across tissues & human protein atlas  \\\\\n",
      "\\bottomrule\n",
      "\\end{tabular}\n",
      "\n",
      "\\begin{table}\n",
      "\\capation{Detailed desctiption for the benchmarking tasks belonging to the family Regulatory functions}\n",
      "\\label{tab:task_descriptions_regulatory_functions}\n",
      "\\centering\n",
      "\\begin{tabular}{llrll}\n",
      "\\toprule\n",
      "Task Name & Type & Size & Description & Origin \\\\\n",
      "\\midrule\n",
      "Gene2gene & binary & 290032 & Pairs of genes with a known association & GenePT \\\\\n",
      "Interactions & regression & 11348 & Number of proteins each gene is known to interact with & human protein atlas  \\\\\n",
      "Long vs short range tf & binary & 174 & Is activation by the TF binary (short range) or linear (long range) & GenePT \\\\\n",
      "N1 network & binary & 1103 & Division of the N1 gene resulatory network into core and peripheral downstreamt effectors & How do Large Language Models understand Genes and Cells \\\\\n",
      "N1 targets & binary & 281 & Genes that are downstream targets in the N1 gene reglatory network & How do Large Language Models understand Genes and Cells \\\\\n",
      "Tf vs non-tf & binary & 2765 & Is the gene known to function as a trascription factor & The Human Transcription Factors \\\\\n",
      "\\bottomrule\n",
      "\\end{tabular}\n",
      "\n"
     ]
    }
   ],
   "source": [
    "for task_family, details in tasks.groupby(tasks[\"Family\"]):\n",
    "    print_task_family_table(task_family, details)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.9"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}