{ "cells": [ { "cell_type": "markdown", "id": "55e261bb", "metadata": {}, "source": [ "## Visuailzing multiple enrichment analysis results\n", "\n", "Utilizing GSEApy, we present an example of visualizing the outcomes of multiple enrichment analyses. Here, we employ a dataset from a study that examined transcriptomic alterations induced by BK polyomavirus infection in renal tubular epithelial cells ([Assetta et al. 2019](https://doi.org/10.1128/mbio.02354-19))." ] }, { "cell_type": "code", "execution_count": 1, "id": "ce29a422", "metadata": {}, "outputs": [], "source": [ "import gseapy" ] }, { "cell_type": "code", "execution_count": 2, "id": "2743dfe7", "metadata": {}, "outputs": [], "source": [ "import os\n", "import pickle as pkl\n", "\n", "from pydeseq2.dds import DeseqDataSet\n", "from pydeseq2.ds import DeseqStats\n", "from pydeseq2.utils import load_example_data\n", "\n", "import warnings\n", "warnings.filterwarnings('ignore')\n" ] }, { "cell_type": "code", "execution_count": 3, "id": "61388295", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | A1BG | \n", "A1BG-AS1 | \n", "A1CF | \n", "A2M | \n", "A2M-AS1 | \n", "A2ML1 | \n", "A2MP1 | \n", "A3GALT2 | \n", "A4GALT | \n", "A4GNT | \n", "... | \n", "ZWILCH | \n", "ZWINT | \n", "ZXDA | \n", "ZXDB | \n", "ZXDC | \n", "ZYG11A | \n", "ZYG11B | \n", "ZYX | \n", "ZZEF1 | \n", "ZZZ3 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SRR9967595 | \n", "20 | \n", "81 | \n", "1 | \n", "0 | \n", "22 | \n", "0 | \n", "0 | \n", "0 | \n", "669 | \n", "0 | \n", "... | \n", "1055 | \n", "1034 | \n", "295 | \n", "363 | \n", "1053 | \n", "96 | \n", "2297 | \n", "2381 | \n", "1801 | \n", "2806 | \n", "
SRR9967596 | \n", "27 | \n", "80 | \n", "1 | \n", "1 | \n", "14 | \n", "0 | \n", "0 | \n", "0 | \n", "504 | \n", "0 | \n", "... | \n", "901 | \n", "1023 | \n", "299 | \n", "293 | \n", "868 | \n", "80 | \n", "1998 | \n", "2238 | \n", "1521 | \n", "2481 | \n", "
SRR9967597 | \n", "15 | \n", "82 | \n", "0 | \n", "3 | \n", "18 | \n", "0 | \n", "0 | \n", "0 | \n", "513 | \n", "0 | \n", "... | \n", "1307 | \n", "1564 | \n", "257 | \n", "409 | \n", "1040 | \n", "84 | \n", "2527 | \n", "1895 | \n", "1939 | \n", "2901 | \n", "
SRR9967598 | \n", "9 | \n", "44 | \n", "1 | \n", "1 | \n", "7 | \n", "1 | \n", "0 | \n", "0 | \n", "488 | \n", "0 | \n", "... | \n", "978 | \n", "1779 | \n", "66 | \n", "123 | \n", "612 | \n", "108 | \n", "1072 | \n", "858 | \n", "1228 | \n", "1927 | \n", "
SRR9967599 | \n", "23 | \n", "77 | \n", "0 | \n", "2 | \n", "10 | \n", "0 | \n", "0 | \n", "3 | \n", "721 | \n", "1 | \n", "... | \n", "1650 | \n", "2778 | \n", "135 | \n", "183 | \n", "855 | \n", "121 | \n", "1769 | \n", "1016 | \n", "1484 | \n", "2843 | \n", "
5 rows × 29744 columns
\n", "\n", " | Run | \n", "Assay Type | \n", "AvgSpotLen | \n", "BioProject | \n", "BioSample | \n", "cell_source | \n", "Cell_type | \n", "Center Name | \n", "Consent | \n", "DATASTORE filetype | \n", "... | \n", "MBytes | \n", "Organism | \n", "Platform | \n", "ReleaseDate | \n", "sample_acc | \n", "Sample Name | \n", "source_name | \n", "SRA Study | \n", "time_point | \n", "treatment | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SRR9967595 | \n", "SRR9967595 | \n", "RNA-Seq | \n", "100 | \n", "PRJNA560236 | \n", "SAMN12572476 | \n", "13 months old female | \n", "Primary Human Renal Epithelial Cells (ATCC) | \n", "GEO | \n", "public | \n", "fastq,sra | \n", "... | \n", "2404 | \n", "Homo sapiens | \n", "ILLUMINA | \n", "2019-08-15T00:00:00Z | \n", "SRS5268041 | \n", "GSM4034946 | \n", "BK infected cells at 3 days post infection | \n", "SRP218354 | \n", "at 3 days post infection | \n", "BK polyomavirus (BKPyV) | \n", "
SRR9967596 | \n", "SRR9967596 | \n", "RNA-Seq | \n", "100 | \n", "PRJNA560236 | \n", "SAMN12572509 | \n", "13 months old female | \n", "Primary Human Renal Epithelial Cells (ATCC) | \n", "GEO | \n", "public | \n", "fastq,sra | \n", "... | \n", "1997 | \n", "Homo sapiens | \n", "ILLUMINA | \n", "2019-08-15T00:00:00Z | \n", "SRS5268042 | \n", "GSM4034947 | \n", "BK infected cells at 3 days post infection | \n", "SRP218354 | \n", "at 3 days post infection | \n", "BK polyomavirus (BKPyV) | \n", "
SRR9967597 | \n", "SRR9967597 | \n", "RNA-Seq | \n", "100 | \n", "PRJNA560236 | \n", "SAMN12572508 | \n", "13 months old female | \n", "Primary Human Renal Epithelial Cells (ATCC) | \n", "GEO | \n", "public | \n", "fastq,sra | \n", "... | \n", "2375 | \n", "Homo sapiens | \n", "ILLUMINA | \n", "2019-08-15T00:00:00Z | \n", "SRS5268043 | \n", "GSM4034948 | \n", "BK infected cells at 3 days post infection | \n", "SRP218354 | \n", "at 3 days post infection | \n", "BK polyomavirus (BKPyV) | \n", "
SRR9967598 | \n", "SRR9967598 | \n", "RNA-Seq | \n", "100 | \n", "PRJNA560236 | \n", "SAMN12572507 | \n", "13 months old female | \n", "Primary Human Renal Epithelial Cells (ATCC) | \n", "GEO | \n", "public | \n", "fastq,sra | \n", "... | \n", "1921 | \n", "Homo sapiens | \n", "ILLUMINA | \n", "2019-08-15T00:00:00Z | \n", "SRS5268044 | \n", "GSM4034949 | \n", "BK infected cells at 6 days post infection | \n", "SRP218354 | \n", "at 6 days post infection | \n", "BK polyomavirus (BKPyV) | \n", "
SRR9967599 | \n", "SRR9967599 | \n", "RNA-Seq | \n", "100 | \n", "PRJNA560236 | \n", "SAMN12572506 | \n", "13 months old female | \n", "Primary Human Renal Epithelial Cells (ATCC) | \n", "GEO | \n", "public | \n", "fastq,sra | \n", "... | \n", "2676 | \n", "Homo sapiens | \n", "ILLUMINA | \n", "2019-08-15T00:00:00Z | \n", "SRS5268045 | \n", "GSM4034950 | \n", "BK infected cells at 6 days post infection | \n", "SRP218354 | \n", "at 6 days post infection | \n", "BK polyomavirus (BKPyV) | \n", "
5 rows × 29 columns
\n", "\n", " | baseMean | \n", "log2FoldChange | \n", "lfcSE | \n", "stat | \n", "pvalue | \n", "padj | \n", "
---|---|---|---|---|---|---|
A1BG | \n", "15.356750 | \n", "0.019922 | \n", "0.380606 | \n", "0.052344 | \n", "9.582549e-01 | \n", "0.974228 | \n", "
A1BG-AS1 | \n", "79.427946 | \n", "-0.747451 | \n", "0.292659 | \n", "-2.554004 | \n", "1.064922e-02 | \n", "0.032686 | \n", "
A1CF | \n", "0.685369 | \n", "-1.268784 | \n", "1.636031 | \n", "-0.775526 | \n", "4.380292e-01 | \n", "NaN | \n", "
A2M | \n", "0.968656 | \n", "0.189368 | \n", "1.209550 | \n", "0.156561 | \n", "8.755908e-01 | \n", "NaN | \n", "
A2M-AS1 | \n", "12.146683 | \n", "-1.006216 | \n", "0.439510 | \n", "-2.289404 | \n", "2.205589e-02 | \n", "0.059017 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
ZYG11A | \n", "84.048757 | \n", "1.337741 | \n", "0.262999 | \n", "5.086480 | \n", "3.647705e-07 | \n", "0.000004 | \n", "
ZYG11B | \n", "1863.055526 | \n", "-0.436978 | \n", "0.184829 | \n", "-2.364225 | \n", "1.806783e-02 | \n", "0.050254 | \n", "
ZYX | \n", "1102.044658 | \n", "-0.545409 | \n", "0.301693 | \n", "-1.807829 | \n", "7.063307e-02 | \n", "0.147662 | \n", "
ZZEF1 | \n", "1504.948093 | \n", "-0.016638 | \n", "0.169712 | \n", "-0.098035 | \n", "9.219047e-01 | \n", "0.951360 | \n", "
ZZZ3 | \n", "2551.864972 | \n", "0.034200 | \n", "0.137628 | \n", "0.248499 | \n", "8.037484e-01 | \n", "0.872939 | \n", "
29744 rows × 6 columns
\n", "