2e:null 2f:["$","title",null,{"children":"mSigPortal Integration - mSigSDK Visualizations | Aaron Ge | Observable"}] 34:[] 32:{"id":"0e1ee3d5a188a2e8","slug":"msigportal-integration-msigsdk-visualizations","title":"mSigPortal Integration - mSigSDK Visualizations","thumbnail":"d24400c7f51148152d75d53b7b56ac0e4e9e285511284e9f02fcb35f296c1cd9","access_level":"public","create_time":"$D2023-03-20T11:44:15.904Z","update_time":"$D2026-05-11T13:39:45.583Z","view_time":null,"first_public_time":"$D2023-03-20T11:44:15.904Z","fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"67a652fa41ec3550","login":"aaronge-2020","name":"Aaron Ge","avatar_url":"https://avatars-next.observableusercontent.com/d8cc425d5e64ef116e24ef6e701909b44669b7a3088a311d2de0215ac50324e2","tier":"starter_2024"},"version":256,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"152d0a566a39ccad","login":"aaronge-2020","name":"Aaron Ge","avatar_url":"https://avatars-next.observableusercontent.com/d8cc425d5e64ef116e24ef6e701909b44669b7a3088a311d2de0215ac50324e2","tier":null}],"members":[{"type":"individual","id":"152d0a566a39ccad","login":"aaronge-2020","name":"Aaron Ge","avatar_url":"https://avatars-next.observableusercontent.com/d8cc425d5e64ef116e24ef6e701909b44669b7a3088a311d2de0215ac50324e2","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"mSigPortal Integration - mSigSDK Visualizations","cells":[{"id":0,"value":"# mSigPortal Integration - mSigSDK Visualizations","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":11,"value":"### Importing the module","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":13,"value":"module = import(\"https://episphere.github.io/msig/main.js\")\n// module = import('http://127.0.0.1:5500/main.js')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"mSigSDK = module.mSigSDK","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"## Dataset Summary","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":114,"value":"projectData = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSpectrumData(\n \"PCAWG\",\n null,\n \"WGS\",\n null,\n \"SBS\",\n 96,\n);","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7,"value":"

\n","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":17,"value":"mSigSDK.mSigPortal.mSigPortalPlots.plotProfilerSummary(\"PCAWG\",\"WGS\",\"Lung-AdenoCA\", 741);\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":120,"value":"

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":111,"value":"mSigSDK.mSigPortal.mSigPortalPlots.plotProjectMutationalBurdenByCancerType(projectData, \"cancerTypeSummary\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":23,"value":"## Mutational Spectra","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":27,"value":"

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":20,"value":"mutationalSpectrumData = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSpectrumData(\n \"PCAWG\",\n [\"SP99181\", \"SP98955\"],\n \"WGS\",\n \"Liver-HCC\",\n \"SBS\",\n 96,\n);","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":37,"value":"mSigSDK.mSigPortal.mSigPortalPlots.plotPatientMutationalSpectrum(mutationalSpectrumData, \"mutationalSpectrumMatrix\");","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":52,"value":"## Obtaining Visualization Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":55,"value":"cancerType = \"Lung-AdenoCA\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":57,"value":"extractedData = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSpectrumData(\n \"PCAWG\",\n null,\n \"WGS\",\n cancerType,\n \"SBS\",\n 96,\n);","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":89,"value":"## Force Directed Tree","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":221,"value":"## Notes\n1) Have the ability to search the sample name\n2) Have the entire tree expanded in the beginning\n3) Implemented a colorscale for cosine-similarity","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":97,"value":"

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":91,"value":"formattedClusters = mSigSDK.mSigPortal.mSigPortalPlots.plotForceDirectedTree(extractedData, \"PCAWG\",\"WGS\",cancerType, \"forceDirectedTree\");","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":71,"value":"## Cosine Similarity Matrix","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":76,"value":"

\n","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":73,"value":"cosSimilarity = mSigSDK.mSigPortal.mSigPortalPlots.plotCosineSimilarityHeatMap(extractedData, \"PCAWG\", \"WGS\", \"Lung-AdenoCA\", \"cosineSimilarityHeatMap\", true);","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":99,"value":"## UMAP Visualizations","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":101,"value":"

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":104,"value":"embeddings = mSigSDK.mSigPortal.mSigPortalPlots.plotUMAPVisualization(extractedData, \"PCAWG\", \"umapVisualization\", 3, 0.1, 15)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":182,"value":"## Visualizing Signature Activity Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":184,"value":"data = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSignatureActivityData('PCAWG','WGS','COSMIC_v3_Signatures_GRCh37_SBS96','',100000)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":186,"value":"

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":188,"value":"mSigSDK.mSigPortal.mSigPortalPlots.plotSignatureActivityDataBy(\"testDiv\", data, 'cancer');","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":194,"value":"

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":192,"value":"mSigSDK.mSigPortal.mSigPortalPlots.plotSignatureAssociations(\"associations\", data, 'SBS1', 'SBS2')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":198,"value":"

","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":200,"value":"mSigSDK.mSigPortal.mSigPortalPlots.plotMSPrevalenceData(\"prevalence\", data)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W34","stdlib":"1","titling":"auto"}} 33:"$32:body"