################################################### ### chunk number 1: ################################################### options(width=50) ################################################### ### chunk number 2: ################################################### library(GenomeGraphs) ################################################### ### chunk number 3: ################################################### mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") ################################################### ### chunk number 4: ################################################### gene <- makeGene(id = "ENSG00000095203", type="ensembl_gene_id", biomart = mart) gdPlot(gene) ################################################### ### chunk number 5: ################################################### transcript <- makeTranscript(id = "ENSG00000095203", type="ensembl_gene_id", biomart = mart) gdPlot(list(gene, transcript)) ################################################### ### chunk number 6: ################################################### plusStrand <- makeGeneRegion(chromosome = 17, start = 30450000, end = 30550000, strand = "+", biomart = mart) genomeAxis <- makeGenomeAxis(add53 = TRUE) gdPlot(list(genomeAxis, plusStrand)) ################################################### ### chunk number 7: ################################################### minStrand <- makeGeneRegion( chromosome = 17, start = 30450000, end = 30550000, strand = "-", biomart = mart) ideogram <- makeIdeogram(chromosome = 17) genomeAxis <- makeGenomeAxis(add53=TRUE, add35=TRUE) gdPlot(list(ideogram, plusStrand, genomeAxis, minStrand), minBase = 30450000, maxBase = 30550000) ################################################### ### chunk number 8: ################################################### data("exampleData", package="GenomeGraphs") minbase <- 180292097 maxbase <- 180492096 genesplus <- makeGeneRegion(start = minbase, end = maxbase, strand = "+", chromosome = "3", biomart=mart) genesmin <- makeGeneRegion(start = minbase, end = maxbase, strand = "-", chromosome = "3", biomart=mart) seg <- makeSegmentation(segStart, segEnd, segments, dp = DisplayPars(color = "black", lwd=2,lty = "solid")) cop <- makeGenericArray(intensity = cn, probeStart = probestart, segmentation = seg, dp = DisplayPars(size=3, color = "seagreen", type="dot")) ideog <- makeIdeogram(chromosome = 3) expres <- makeGenericArray(intensity = intensity, probeStart = exonProbePos, dp = DisplayPars(color="darkred", type="point")) genomeAxis <- makeGenomeAxis(add53 = TRUE, add35=TRUE) gdPlot(list(a=ideog,b=expres,c=cop,d=genesplus,e=genomeAxis,f=genesmin), minBase = minbase, maxBase =maxbase, labelCex = 2) ################################################### ### chunk number 9: ################################################### data("unrData", package="GenomeGraphs") title <- makeTitle(text ="ENSG00000009307", color = "darkred") exon <- makeExonArray(intensity = unrData, probeStart = unrPositions[,3], probeEnd=unrPositions[,4], probeId = as.character(unrPositions[,1]), nProbes = unrNProbes, dp = DisplayPars(color = "blue", mapColor = "dodgerblue2"), displayProbesets=FALSE) affyModel.model <- makeGeneModel(start = unrPositions[,3], end = unrPositions[,4]) affyModel <- makeAnnotationTrack(start = unrPositions[,3], end = unrPositions[,4], feature = "gene_model", group = "ENSG00000009307", dp = DisplayPars(gene_model = "darkblue")) gene <- makeGene(id = "ENSG00000009307", biomart = mart) transcript <- makeTranscript( id ="ENSG00000009307" , biomart = mart) legend <- makeLegend(c("affyModel","gene"), fill = c("darkgreen","orange")) rOverlay <- makeRectangleOverlay(start = 115085100, end = 115086500, region = c(3,5), dp = DisplayPars(alpha = .2, fill = "olivedrab1")) gdPlot(list(title, exon, affyModel, gene, transcript, legend), minBase = 115061061, maxBase=115102147, overlay = rOverlay) ################################################### ### chunk number 10: ################################################### yeastMart <- useMart("ensembl", dataset = "scerevisiae_gene_ensembl") minB <- 10000 maxB <- 20000 chrRoman <- as.character(as.roman(1)) grP <- makeGeneRegion(start = minB, end = maxB, strand = "+", chromosome = chrRoman, biomart = yeastMart) grM <- makeGeneRegion(start = minB, end = maxB, strand = "-", chromosome = chrRoman, biomart = yeastMart) gaxis <- makeGenomeAxis( add53 = TRUE, add35 = TRUE) conserv <- yeastCons1[yeastCons1[,1] > minB & yeastCons1[,1] < maxB, ] consTrack <- makeBaseTrack( base = conserv[, 1], value = conserv[,2], dp = DisplayPars(lwd=.2, ylim = c(0, 1.25), color = "darkblue")) gdPlot(list(grP, gaxis, grM, "conservation" = consTrack)) ################################################### ### chunk number 11: ################################################### plotGeneRegion <- function(chr = 1, minB = 9000, maxB = 13000, rot = 0, col = "green") { chrRoman <- as.character(as.roman(1:17)[chr]) grP <- makeGeneRegion(start = minB, end = maxB, strand = "+", chromosome = chrRoman, biomart = yeastMart, dp = DisplayPars(plotId = TRUE, idRotation = rot, idColor = col)) gaxis <- makeGenomeAxis( add53 = TRUE, add35 = TRUE, littleTicks = FALSE) gdPlot(list(grP, gaxis), minBase = minB, maxBase = maxB) } plotGeneRegion(col = "yellow", rot=90) ################################################### ### chunk number 12: ################################################### gdPlot(makeGeneRegion(start = 9000, end = 15000, biomart = yeastMart, strand = "-", chromosome = "I", dp = DisplayPars(plotId=TRUE))) ################################################### ### chunk number 13: ################################################### ga <- makeGenomeAxis() grF <- makeGeneRegion(start = 10000, end = 20000, chromosome = "I", strand = "+", biomart = yeastMart) grR <- makeGeneRegion(start = 10000, end = 20000, chromosome = "I", strand = "-", biomart = yeastMart) bt <- makeBaseTrack(base = yeastCons1[,1], value = yeastCons1[,2]) hr1 <- makeRectangleOverlay(start = 11000, end = 13000) hr2 <- makeRectangleOverlay(start = 15900, end = 16500) gdPlot(list(grF, ga, grR, bt), overlays = list(hr1, hr2)) ################################################### ### chunk number 14: ################################################### ro <- makeRectangleOverlay(start = 11000, end = 13000, region = c(1,3), dp = DisplayPars(color = "green", alpha = .3)) to <- makeTextOverlay("here is some text", xpos = 15000, ypos = .95) gdPlot(list(grF, ga, grR, bt), overlay = c(ro, to)) ################################################### ### chunk number 15: ################################################### roR <- makeRectangleOverlay(start = .1, end = .3, coords = "absolute", dp = DisplayPars(fill = "grey", alpha = .2, lty = "dashed"), region = c(.4,.7)) gdPlot(list(grF, ga, grR, bt), overlays = list(ro, roR)) ################################################### ### chunk number 16: ################################################### data("seqDataEx", package = "GenomeGraphs") str = seqDataEx$david[,"strand"] == 1 biomart = useMart("ensembl", "scerevisiae_gene_ensembl") pList = list("-" = makeGeneRegion(chromosome = "IV", start = 1300000, end = 1310000, strand = "-", biomart = biomart, dp = DisplayPars(plotId = TRUE, idRotation = 0, cex = .5)), makeGenomeAxis(dp = DisplayPars(size = 3)), "+" = makeGeneRegion(chromosome = "IV", start = 1300000, end = 1310000, strand = "+", biomart = biomart, dp = DisplayPars(plotId = TRUE, idRotation = 0, cex = .5)), "Nagalakshmi" = makeBaseTrack(base = seqDataEx$snyder[, "location"], value = seqDataEx$snyder[, "counts"], dp = DisplayPars(lwd = .3, color = "darkblue", ylim = c(0,300))), "David +" = makeGenericArray(probeStart = seqDataEx$david[str, "location"], intensity = seqDataEx$david[str, "expr", drop=FALSE], dp = DisplayPars(pointSize = .5)), "David -" = makeGenericArray(probeStart = seqDataEx$david[!str, "location"], intensity = seqDataEx$david[!str, "expr", drop=FALSE], dp = DisplayPars(color = "darkgreen", pointSize = .5)), "Lee" = makeBaseTrack(base = seqDataEx$nislow[, "location"], value = seqDataEx$nislow[, "evalue"], dp = DisplayPars(color="grey", lwd=.25)), "Conservation" = makeBaseTrack(base = seqDataEx$conservation[, "location"], value = seqDataEx$conservation[, "score"], dp = DisplayPars(color="gold4", lwd=.25))) gdPlot(pList, minBase = 1301500, maxBase = 1302500, overlay = makeRectangleOverlay(start = 1302105, end = 1302190, region = c(4,8), dp = DisplayPars(alpha = .2))) ################################################### ### chunk number 17: ################################################### setPar(pList$Lee@dp, "type", "h") setPar(pList$Lee@dp, "color", "limegreen") setPar(pList$Lee@dp, "lwd", 2) gdPlot(pList, minBase = 1301500, maxBase = 1302500, overlay = makeRectangleOverlay(start = 1302105, end = 1302190, region = c(4,8), dp = DisplayPars(alpha = .2)))