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b/notebooks/plot_reactome.ipynb |
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{ |
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"cells": [ |
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{ |
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"cell_type": "code", |
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"execution_count": 1, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"%load_ext autoreload\n", |
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"%autoreload 2\n", |
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"\n", |
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"%matplotlib inline" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 2, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"import sys" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 3, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"sys.path.append('..')\n", |
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"\n", |
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"from pyMultiOmics.plots import download_reactome_diagram\n", |
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"from pyMultiOmics.constants import HOMO_SAPIENS" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 4, |
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"metadata": {}, |
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"outputs": [ |
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{ |
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"name": "stderr", |
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"output_type": "stream", |
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"text": [ |
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"2022-03-24 14:49:06.061 | DEBUG | pyMultiOmics.plots:send_reactome_expression_data:86 - POSTing expression data to Reactome Analysis Service: https://reactome.org/AnalysisService/identifiers/?interactors=false&species=Homo%20sapiens&sortBy=ENTITIES_PVALUE&order=ASC&resource=TOTAL&pValue=1&includeDisease=true\n", |
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"2022-03-24 14:49:07.812 | DEBUG | pyMultiOmics.plots:send_reactome_expression_data:90 - Received HTTP status code: 200\n", |
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"2022-03-24 14:49:07.817 | DEBUG | pyMultiOmics.plots:parse_reactome_json:115 - Received expression analysis token: MjAyMjAzMjQxMDIxMjdfNDExOTA%3D\n", |
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"2022-03-24 14:49:08.834 | DEBUG | pyMultiOmics.plots:download_reactome_diagram:67 - Image saved to reactome.png\n" |
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] |
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} |
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], |
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"source": [ |
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"stId = 'R-HSA-70921'\n", |
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"out_file = 'reactome.png'\n", |
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"exp_dict = {\n", |
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" 'C00135': 1.0, # kegg\n", |
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" 'C01342': 2.0, # kegg\n", |
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" '30817': 3.0, # ChEBI\n", |
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" 'HAL': 4.0, # gene name\n", |
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" 'ENSG00000172508': 5.0, # ensembl\n", |
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" 'Q96NU7': 6.0 # uniprot\n", |
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"}\n", |
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"\n", |
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"download_reactome_diagram(stId, out_file, species=HOMO_SAPIENS, expression_dict=exp_dict)" |
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] |
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}, |
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{ |
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"cell_type": "markdown", |
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"metadata": {}, |
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"source": [ |
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"" |
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] |
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} |
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], |
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"metadata": { |
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"kernelspec": { |
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"display_name": "Python 3 (ipykernel)", |
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"language": "python", |
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"name": "python3" |
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}, |
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"language_info": { |
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"codemirror_mode": { |
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"name": "ipython", |
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"version": 3 |
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}, |
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"file_extension": ".py", |
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"mimetype": "text/x-python", |
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"name": "python", |
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"nbconvert_exporter": "python", |
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"pygments_lexer": "ipython3", |
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"version": "3.10.1" |
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} |
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}, |
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"nbformat": 4, |
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"nbformat_minor": 4 |
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} |