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])
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.
