Public
Edited
Jan 3
module = import("https://episphere.github.io/msig/main.js")
// module = import("http://127.0.0.1:5500/main.js")
mSigSDK = module.mSigSDK
viewof WGS_data_tsv = Inputs.file({label: "Input MAF file here: ", accept: ".maf", required: true, multiple: true})
// Asynchronous computation for WGS_data
WGS_data = await Promise.all(WGS_data_tsv.map(file => file.tsv()));
viewof tsvfile = Inputs.file({label: "Input bed file here: ", accept: ".bed", required: true})
bed_file = tsvfile.tsv()
// viewof numberOfPanelPatients = Inputs.range([1, 11], {value: 2, step: 1, label: "Number of Patients to Downsample"})
msk_impact_panel_data = mSigSDK.userData.convertWGStoPanel(WGS_data, bed_file)
mutational_spectra_panel = mSigSDK.userData.convertMatrix(msk_impact_panel_data, "center")
viewof numberOfWGSPatients = Inputs.range([1, 11], {value: WGS_data.length, step: 1, label: "Number of WGS Patients"})
WGS_data_mutational_spectra = mSigSDK.userData.convertMatrix(WGS_data.slice(0,numberOfWGSPatients), "Center")
JSONData = mSigSDK.userData.convertMutationalSpectraIntoJSON(WGS_data.slice(0,numberOfWGSPatients), WGS_data_mutational_spectra, "Center")
mSigSDK.mSigPortal.mSigPortalPlots.plotPatientMutationalSpectrum(JSONData, "mutationalSpectrumMatrixWGSICGC");
cosSimilarityICGC = mSigSDK.mSigPortal.mSigPortalPlots.plotCosineSimilarityHeatMap(JSONData ,"ICGC", "WGS", "COAD-US", "cosineSimilarityHeatMapICGC", true, "RdBu", true);
mutationalSignatures = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSignaturesData("WGS", "COSMIC_v3_Signatures_GRCh37_SBS96", "SBS", 96, 10000)
mutationalSignaturesExtracted = await mSigSDK.mSigPortal.mSigPortalData.extractMutationalSpectra(mutationalSignatures, "signatureName")
extractedPatientData = mSigSDK.mSigPortal.mSigPortalData.extractMutationalSpectra(JSONData)
nnlsExposures = mSigSDK.signatureFitting.fitMutationalSpectraToSignatures(mutationalSignaturesExtracted, extractedPatientData, { exposureThreshold: 0.02, exposureType: "absolute" })
mSigSDK.signatureFitting.plotPatientMutationalSignaturesExposure(nnlsExposures[Object.keys(nnlsExposures)[0]], "exposureGraph", Object.keys(nnlsExposures)[0])
One platform to build and deploy the best data apps
Experiment and prototype by building visualizations in live JavaScript notebooks. Collaborate with your team and decide which concepts to build out.
Use Observable Framework to build data apps locally. Use data loaders to build in any language or library, including Python, SQL, and R.
Seamlessly deploy to Observable. Test before you ship, use automatic deploy-on-commit, and ensure your projects are always up-to-date.