The avatar for @aaronge-2020
Aaron Ge
Public
Edited
Jan 2
Insert cell
Insert cell
Insert cell
// module = import("https://episphere.github.io/msig/main.js")
module = import('http://127.0.0.1:5500/main.js')
Insert cell
mSigSDK = module.mSigSDK
Insert cell
Insert cell
projectData = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSpectrumData(
"PCAWG",
null,
"WGS",
null,
"SBS",
96,
);
Insert cell
Insert cell
mSigSDK.mSigPortal.mSigPortalPlots.plotProfilerSummary("PCAWG","WGS","Lung-AdenoCA", 741);

Insert cell
Insert cell
mSigSDK.mSigPortal.mSigPortalPlots.plotProjectMutationalBurdenByCancerType(projectData, "cancerTypeSummary")
Insert cell
Insert cell
Insert cell
mutationalSpectrumData = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSpectrumData(
"PCAWG",
["SP99181", "SP98955"],
"WGS",
"Liver-HCC",
"SBS",
96,
);
Insert cell
mSigSDK.mSigPortal.mSigPortalPlots.plotPatientMutationalSpectrum(mutationalSpectrumData, "mutationalSpectrumMatrix");
Insert cell
Insert cell
cancerType = "Lung-AdenoCA"
Insert cell
extractedData = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSpectrumData(
"PCAWG",
null,
"WGS",
cancerType,
"SBS",
96,
);
Insert cell
Insert cell
Insert cell
Insert cell
formattedClusters = mSigSDK.mSigPortal.mSigPortalPlots.plotForceDirectedTree(extractedData, "PCAWG","WGS",cancerType, "forceDirectedTree");
Insert cell
Insert cell
Insert cell
cosSimilarity = mSigSDK.mSigPortal.mSigPortalPlots.plotCosineSimilarityHeatMap(extractedData, "PCAWG", "WGS", "Lung-AdenoCA", "cosineSimilarityHeatMap", true);
Insert cell
Insert cell
Insert cell
embeddings = mSigSDK.mSigPortal.mSigPortalPlots.plotUMAPVisualization(extractedData, "PCAWG", "umapVisualization", 3, 0.1, 15)
Insert cell
Insert cell
data = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSignatureActivityData('PCAWG','WGS','COSMIC_v3_Signatures_GRCh37_SBS96','',100000)
Insert cell
Insert cell
mSigSDK.mSigPortal.mSigPortalPlots.plotSignatureActivityDataBy("testDiv", data, 'cancer');
Insert cell
Insert cell
mSigSDK.mSigPortal.mSigPortalPlots.plotSignatureAssociations("associations", data, 'SBS1', 'SBS2')
Insert cell
Insert cell
mSigSDK.mSigPortal.mSigPortalPlots.plotMSPrevalenceData("prevalence", data)
Insert cell

Purpose-built for displays of data

Observable is your go-to platform for exploring data and creating expressive data visualizations. Use reactive JavaScript notebooks for prototyping and a collaborative canvas for visual data exploration and dashboard creation.
Learn more