{ "cells": [ { "cell_type": "markdown", "id": "b1ac0947", "metadata": {}, "source": [ "# _BRCA_ Heatmap" ] }, { "cell_type": "code", "execution_count": 1, "id": "93b49611", "metadata": {}, "outputs": [], "source": [ "import CanDI.candi as can\n", "import pandas as pd\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", "from mpl_toolkits.axes_grid1 import make_axes_locatable\n" ] }, { "cell_type": "markdown", "id": "3f9e2439", "metadata": {}, "source": [ "### Cancer Object Instantiation\n", "We're interested in cross referencing some data in breast and ovarian cancer so instantiate cancer objects as follows.\n", "To double check the object instantiation I check the length of the depmap_id vectors. This lets me know we're able to index other datasets correctly" ] }, { "cell_type": "code", "execution_count": 2, "id": "c220005a", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "74\n", "83\n" ] } ], "source": [ "ov = can.Cancer(\"Ovarian Cancer\")\n", "br = can.Cancer(\"Breast Cancer\")\n", "\n", "#Number of Ovarian Cell lines\n", "print(len(ov.depmap_ids))\n", "#Number of Breast Cell Lines\n", "print(len(br.depmap_ids))" ] }, { "cell_type": "markdown", "id": "659d1805", "metadata": {}, "source": [ "### Subsetting by mutation status\n", "\n", "Explicitly load mutations into memory.This only needs to be done once\n", "You will be done prompted to load a given dataset if using operations that act\n", "on that dataset and it is not in memory." ] }, { "cell_type": "code", "execution_count": 3, "id": "d098ddf9", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | gene | \n", "Entrez_Gene_Id | \n", "NCBI_Build | \n", "Chromosome | \n", "Start_position | \n", "End_position | \n", "Strand | \n", "Variant_Classification | \n", "Variant_Type | \n", "Reference_Allele | \n", "... | \n", "isCOSMIChotspot | \n", "COSMIChsCnt | \n", "ExAC_AF | \n", "Variant_annotation | \n", "CGA_WES_AC | \n", "HC_AC | \n", "RD_AC | \n", "RNAseq_AC | \n", "SangerWES_AC | \n", "WGS_AC | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "VPS13D | \n", "55187 | \n", "37 | \n", "1 | \n", "12359347 | \n", "12359347 | \n", "+ | \n", "Nonsense_Mutation | \n", "SNP | \n", "C | \n", "... | \n", "False | \n", "0.0 | \n", "NaN | \n", "damaging | \n", "34:213 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "34:221 | \n", "NaN | \n", "
| 1 | \n", "AADACL4 | \n", "343066 | \n", "37 | \n", "1 | \n", "12726308 | \n", "12726322 | \n", "+ | \n", "In_Frame_Del | \n", "DEL | \n", "CTGGCGTGACGCCAT | \n", "... | \n", "False | \n", "3.0 | \n", "NaN | \n", "other non-conserving | \n", "57:141 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "9:0 | \n", "28:32 | \n", "
| 2 | \n", "IFNLR1 | \n", "163702 | \n", "37 | \n", "1 | \n", "24484172 | \n", "24484172 | \n", "+ | \n", "Silent | \n", "SNP | \n", "G | \n", "... | \n", "False | \n", "0.0 | \n", "NaN | \n", "silent | \n", "118:0 | \n", "NaN | \n", "NaN | \n", "10:0 | \n", "118:0 | \n", "18:0 | \n", "
| 3 | \n", "TMEM57 | \n", "55219 | \n", "37 | \n", "1 | \n", "25785018 | \n", "25785019 | \n", "+ | \n", "Frame_Shift_Ins | \n", "INS | \n", "- | \n", "... | \n", "False | \n", "0.0 | \n", "NaN | \n", "damaging | \n", "NaN | \n", "NaN | \n", "NaN | \n", "6:28 | \n", "NaN | \n", "NaN | \n", "
| 4 | \n", "ZSCAN20 | \n", "7579 | \n", "37 | \n", "1 | \n", "33954141 | \n", "33954141 | \n", "+ | \n", "Missense_Mutation | \n", "SNP | \n", "T | \n", "... | \n", "False | \n", "0.0 | \n", "NaN | \n", "other non-conserving | \n", "28:62 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "27:61 | \n", "NaN | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 1230240 | \n", "SLC39A4 | \n", "55630 | \n", "37 | \n", "8 | \n", "145641991 | \n", "145641991 | \n", "+ | \n", "Silent | \n", "SNP | \n", "C | \n", "... | \n", "False | \n", "0.0 | \n", "0.000017 | \n", "silent | \n", "52:23 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
| 1230241 | \n", "TAL2 | \n", "6887 | \n", "37 | \n", "9 | \n", "108424778 | \n", "108424778 | \n", "+ | \n", "Start_Codon_SNP | \n", "SNP | \n", "A | \n", "... | \n", "False | \n", "0.0 | \n", "NaN | \n", "damaging | \n", "27:0 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
| 1230242 | \n", "TRO | \n", "7216 | \n", "37 | \n", "X | \n", "54955098 | \n", "54955098 | \n", "+ | \n", "Silent | \n", "SNP | \n", "C | \n", "... | \n", "False | \n", "0.0 | \n", "NaN | \n", "silent | \n", "5:16 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
| 1230243 | \n", "USP51 | \n", "158880 | \n", "37 | \n", "X | \n", "55514703 | \n", "55514703 | \n", "+ | \n", "Missense_Mutation | \n", "SNP | \n", "G | \n", "... | \n", "False | \n", "0.0 | \n", "NaN | \n", "other non-conserving | \n", "23:0 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
| 1230244 | \n", "C1GALT1C1 | \n", "29071 | \n", "37 | \n", "X | \n", "119760406 | \n", "119760406 | \n", "+ | \n", "Missense_Mutation | \n", "SNP | \n", "T | \n", "... | \n", "False | \n", "0.0 | \n", "NaN | \n", "other non-conserving | \n", "28:0 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
1230245 rows × 32 columns
\n", "