### R code from vignette source 'Introduction_to_caOmicsV.Rnw' ################################################### ### code chunk number 1: caOmicsVBioMatrixLayoutDemo ################################################### library(caOmicsV) data(biomatrixPlotDemoData) plotBioMatrix(biomatrixPlotDemoData, summaryType="text") bioMatrixLegend(heatmapNames=c("RNASeq", "miRNASeq"), categoryNames=c("Methyl H", "Methyl L"), binaryNames=c("CN LOSS", "CN Gain"), heatmapMin=-3, heatmapMax=3, colorType="BlueWhiteRed") ################################################### ### code chunk number 2: caOmicsVbionetCircosLayoutDemo ################################################### library(caOmicsV) data(bionetPlotDemoData) plotBioNetCircos(bionetPlotDemoData) dataNames <- c("Tissue Type", "RNASeq", "miRNASeq", "Methylation", "CNV") bioNetLegend(dataNames, heatmapMin=-3, heatmapMax=3) ################################################### ### code chunk number 3: caOmicsVDemoData ################################################### library(caOmicsV) data(biomatrixPlotDemoData) names(biomatrixPlotDemoData) data(bionetPlotDemoData) names(bionetPlotDemoData) ################################################### ### code chunk number 4: bioMatrixDemoData ################################################### library(caOmicsV) data(biomatrixPlotDemoData) dataSet <- biomatrixPlotDemoData names(dataSet) ################################################### ### code chunk number 5: InitializeBioMatrix ################################################### numOfGenes <- length(dataSet$geneNames); numOfSamples <- length(dataSet$sampleNames); numOfPhenotypes <- nrow(dataSet$sampleInfo)-1; numOfHeatmap <- length(dataSet$heatmapData); numOfSummary <- length(dataSet$summaryData); phenotypes <- rownames(dataSet$sampleInfo)[-1]; sampleHeight <- 0.4; sampleWidth <- 0.1; samplePadding <- 0.025; geneNameWidth <- 1; sampleNameHeight <- 2.5; remarkWidth <- 2; summaryWidth <- 1; rowPadding <- 0.1; initializeBioMatrixPlot(numOfGenes, numOfSamples, numOfPhenotypes, sampleHeight, sampleWidth, samplePadding, rowPadding, geneNameWidth, remarkWidth, summaryWidth, sampleNameHeight) caOmicsVColors <- getCaOmicsVColors() png("caOmicsVbioMatrixLayoutDemo.png", height=8, width=12, unit="in", res=300, type="cairo") par(cex=0.75) showBioMatrixPlotLayout(dataSet$geneNames,dataSet$sampleNames, phenotypes) ################################################### ### code chunk number 6: PlotBioMatrixPhenotype ################################################### head(dataSet$sampleInfo)[,1:3] rowIndex <- 2; sampleGroup <- as.character(dataSet$sampleInfo[rowIndex,]) sampleTypes <- unique(sampleGroup) sampleColors <- rep("blue", length(sampleGroup)); sampleColors[grep("Tumor", sampleGroup)] <- "red" rowNumber <- 1 areaName <- "phenotype" plotBioMatrixSampleData(rowNumber, areaName, sampleColors); geneLabelX <- getBioMatrixGeneLabelWidth() maxAreaX <- getBioMatrixDataAreaWidth() legendH <- getBioMatrixLegendHeight() plotAreaH <- getBioMatrixPlotAreaHeigth() sampleH<- getBioMatrixSampleHeight() sampleLegendX <- geneLabelX + maxAreaX sampleLegendY <- plotAreaH + legendH - length(sampleTypes)*sampleH colors <- c("blue", "red") legend(sampleLegendX, sampleLegendY, legend=sampleTypes, fill=colors, bty="n", xjust=0) ################################################### ### code chunk number 7: PlotBioMatrixHeatmap ################################################### heatmapData <- as.matrix(dataSet$heatmapData[[1]][,]); plotBioMatrixHeatmap(heatmapData, maxValue=3, minValue=-3) heatmapData <- as.matrix(dataSet$heatmapData[[2]][,]) plotBioMatrixHeatmap(heatmapData, topAdjust=sampleH/2, maxValue=3, minValue=-3); secondNames <- as.character(dataSet$secondGeneNames) textColors <- rep(caOmicsVColors[3], length(secondNames)); plotBioMatrixRowNames(secondNames, "omicsData", textColors, side="right", skipPlotColumns=0); ################################################### ### code chunk number 8: PlotBioMatrixCategoryData ################################################### categoryData <- dataSet$categoryData[[1]] totalCategory <- length(unique(as.numeric(dataSet$categoryData[[1]]))) plotColors <- rev(getCaOmicsVColors()) plotBioMatrixCategoryData(categoryData, areaName="omicsData", sampleColors=plotColors[1:totalCategory]) ################################################### ### code chunk number 9: PlotBioMatrixBinaryData ################################################### binaryData <- dataSet$binaryData[[1]]; plotBioMatrixBinaryData(binaryData, sampleColor=caOmicsVColors[4]); binaryData <- dataSet$binaryData[[2]]; plotBioMatrixBinaryData(binaryData, sampleColor=caOmicsVColors[3]) ################################################### ### code chunk number 10: PlotBioMatrixSummaryData ################################################### summaryData <- dataSet$summaryInfo[[1]][, 2]; summaryTitle <- colnames(dataSet$summaryInfo[[1]])[2]; remarkWidth <- getBioMatrixRemarkWidth(); sampleWidth <- getBioMatrixSampleWidth(); col2skip <- remarkWidth/2/sampleWidth + 2; plotBioMatrixRowNames(summaryTitle, areaName="phenotype", colors="black", side="right", skipPlotColumns=col2skip); plotBioMatrixRowNames(summaryData, "omicsData", colors=caOmicsVColors[3], side="right", skipPlotColumns=col2skip) ################################################### ### code chunk number 11: AddBioMatrixLegend ################################################### bioMatrixLegend(heatmapNames=c("RNASeq", "miRNASeq"), categoryNames=c("Methyl H", "Methyl L"), binaryNames=c("CN LOSS", "CN Gain"), heatmapMin=-3, heatmapMax=3, colorType="BlueWhiteRed") dev.off() ################################################### ### code chunk number 12: BioNetCircosDemoData ################################################### library(caOmicsV) data(bionetPlotDemoData) dataSet <- bionetPlotDemoData sampleNames <- dataSet$sampleNames geneNames <- dataSet$geneNames numOfSamples <- length(sampleNames) numOfSampleInfo <- nrow(dataSet$sampleInfo) - 1 numOfSummary <- ifelse(dataSet$summaryByRow, 0, col(dataSet$summaryInfo)-1) numOfHeatmap <- length(dataSet$heatmapData) numOfCategory <- length(dataSet$categoryData) numOfBinary <- length(dataSet$binaryData) expr <- dataSet$heatmapData[[1]] bioNet <- bc3net(expr) ################################################### ### code chunk number 13: InitializeBioNetCircos ################################################### widthOfSample <- 100 widthBetweenNode <- 3 lengthOfRadius <- 10 dataNum <- sum(numOfSampleInfo, numOfSummary, numOfHeatmap, numOfCategory, numOfBinary) trackheight <- 1.5 widthOfPlotArea <- dataNum*2*trackheight initializeBioNetCircos(bioNet, numOfSamples, widthOfSample, lengthOfRadius, widthBetweenNode, widthOfPlotArea) caOmicsVColors <- getCaOmicsVColors() supportedType <- getCaOmicsVPlotTypes() par(cex=0.75) showBioNetNodesLayout() ################################################### ### code chunk number 14: BioNetCircosNodeLayout ################################################### par(cex=0.6) onTop <- c(14, 15, 16, 9, 7, 20, 8, 24, 10, 25) labelBioNetNodeNames(nodeList=onTop,labelColor="blue", labelLocation="top", labelOffset = 0.7) onBottom <- c(26, 22, 23, 18, 19, 3, 5) labelBioNetNodeNames(nodeList=onBottom,labelColor="black", labelLocation="bottom", labelOffset = 0.7) onLeft <- c(2, 11, 21, 17) labelBioNetNodeNames(nodeList=onLeft,labelColor="red", labelLocation="left", labelOffset = 0.7) onRight <- c(13, 12, 4, 1, 6) labelBioNetNodeNames(nodeList=onRight,labelColor="brown", labelLocation="right", labelOffset = 0.7) ################################################### ### code chunk number 15: EraseBioNetCircosNodes ################################################### eraseBioNetNode() ################################################### ### code chunk number 16: BioNetCircosBoundary ################################################### inner <- lengthOfRadius/2 outer <- inner + trackheight ################################################### ### code chunk number 17: PlotBioNetCircosPhenotype ################################################### groupInfo <- as.character(dataSet$sampleInfo[2, ]) sampleColors <- rep("blue", numOfSamples); sampleColors[grep("Tumor", groupInfo)] <- "red" plotType=supportedType[1] groupInfo <- matrix(groupInfo, nrow=1) bioNetCircosPlot(dataValues=groupInfo, plotType, outer, inner, sampleColors) inner <- outer + 0.5 outer <- inner + trackheight ################################################### ### code chunk number 18: PlotBioNetCircosHeatmap ################################################### exprData <- dataSet$heatmapData[[1]] plotType <- supportedType[4] bioNetCircosPlot(exprData, plotType, outer, inner, plotColors="BlueWhiteRed", maxValue=3, minValue=-3) inner <- outer + 0.5 outer <- inner + trackheight ################################################### ### code chunk number 19: PlotBioNetCircosCategoryData ################################################### categoryData <- dataSet$categoryData[[1]] plotType <- supportedType[2]; bioNetCircosPlot(categoryData, plotType, outer, inner, plotColors="red") inner <- outer + 0.5 outer <- inner + trackheight ################################################### ### code chunk number 20: PlotBioNetCircosBinaryData ################################################### binaryData <- dataSet$binaryData[[1]] plotType <- supportedType[3] plotColors <- rep(caOmicsVColors[1], ncol(binaryData)) bioNetCircosPlot(binaryData, plotType, outer, inner, plotColors) inner <- outer + 0.5 outer <- inner + trackheight ################################################### ### code chunk number 21: LinkBioNetCircosSamples ################################################### outer <- 2.5 bioNetGraph <- getBioNetGraph() nodeIndex <- which(V(bioNetGraph)$name=="PLVAP") fromSample <- 10 toSample <- 50 plotColors <- "red" linkBioNetSamples(nodeIndex, fromSample, toSample, outer, plotColors) fromSample <- 40 toSample <- 20 plotColors <- "blue" linkBioNetSamples(nodeIndex, fromSample, toSample, outer, plotColors) ################################################### ### code chunk number 22: AddBioNetCircosLegend ################################################### dataNames <- c("Tissue Type", "RNASeq", "Methylation", "CNV") bioNetLegend(dataNames, heatmapMin=-3, heatmapMax=3) ################################################### ### code chunk number 23: sessionInfo ################################################### sessionInfo()