;; This buffer is for notes you don't want to save, and for Lisp evaluation. ;; If you want to create a file, visit that file with C-x C-f, ;; then enter the text in that file's own buffer. .gassign <- function(what) assignInNamespace(ns="Gviz", x=what, value=get(what, envir=globalenv())) assignInNamespace(ns="Gviz", x=".computeGroupRange", value=.computeGroupRange) .dpOrDefault <- Gviz:::.dpOrDefault .getStringDims <- Gviz:::.getStringDims .fontGp <- Gviz:::.fontGp assignInNamespace(ns="Gviz", x=".barsAndLabels", value=.barsAndLabels) .pxResolution <- Gviz:::.pxResolution .getBiotypeColor = Gviz:::.getBiotypeColor assignInNamespace(value=.dpOrDefault, x=".dpOrDefault", ns="Gviz") assignInNamespace(value=.dpOrDefaultFont, x=".dpOrDefaultFont", ns="Gviz") assignInNamespace(value=.fontGp, x=".fontGp", ns="Gviz") library(Biobase) assignInNamespace(ns="Gviz", x=".defaultRange", value=.defaultRange) .dpOrDefault <- Gviz:::.dpOrDefault assignInNamespace(ns="Gviz", x=".arrowBar", value=.arrowBar) .pxResolution <- Gviz:::.pxResolution assignInNamespace(ns="Gviz", x=".boxes", value=.boxes) .dpOrDefault <- Gviz:::.dpOrDefault .getBiotypeColor = Gviz:::.getBiotypeColor .getAnn = Gviz:::.getAnn .getImageMap <- Gviz:::.getImageMap assignInNamespace(ns="Gviz", x=".filledBoxes", value=.filledBoxes) .handleComposite <- Gviz:::.handleComposite assignInNamespace(ns="Gviz", x=".filledArrow", value=.filledArrow) .handleComposite <- Gviz:::.handleComposite assignInNamespace(ns="Gviz", x=".updatePars", value=.updatePars) assignInNamespace(ns="Gviz", x=".handleComposite", value=.handleComposite) assignInNamespace(ns="Gviz", x=".setupTextSize", value=.setupTextSize) .dpOrDefault <- Gviz:::.dpOrDefault vpLocation <- Gviz:::vpLocation .verticalSpace <- Gviz:::.verticalSpace .needsAxis <- Gviz:::.needsAxis .PLOT_TYPES <- Gviz:::.PLOT_TYPES assignInNamespace(ns="Gviz", x="plotTracks", value=plotTracks) .whichStrand <- Gviz:::.whichStrand .recChromosome <- Gviz:::.recChromosome .needsTitle <- Gviz:::.needsTitle .fontGp <- Gviz:::.fontGp drawAxis <- Gviz:::drawAxis .getImageMap <- Gviz:::.getImageMap drawGrid <- Gviz:::drawGrid ImageMap <- Gviz:::ImageMap ## This is all needed for sourcing plotTracks .defaultRange <- Gviz:::.defaultRange setStacks <- Gviz:::setStacks vpLocation <- Gviz:::vpLocation .setupTextSize <- Gviz:::.setupTextSize .needsAxis <- Gviz:::.needsAxis drawAxis <- Gviz:::drawAxis .getImageMap <- Gviz:::.getImageMap drawGrid <- Gviz:::drawGrid ImageMap <- Gviz:::ImageMap .needsTitle <- Gviz:::.needsTitle .whichStrand <- Gviz:::.whichStrand .recChromosome <- Gviz:::.recChromosome assignInNamespace(ns="Gviz", x=".needsTitle", value=.needsTitle) assignInNamespace(ns="Gviz", x=".needsAxis", value=.needsAxis) library(Gviz) data(cyp2b10) dt<-GeneRegionTrack(cyp2b10) plotTracks(dt) plotTracks(dt, showId=T, just.group="left", cex.group=0.8, reverseStrand=F, title.width=1) plotTracks(c(dt), just.group="left", cex.group=1, reverseStrand=F, title.width=1, geneSymbols="symbol", fontface.group="bold.italic", fontcolor.group="red", showExonId=F, fontcolor.item=1, from=25897620-500, to=25897855, fontfamily="serif", fontfamily.item="sans", showId=T, just.group="left") plotTracks(c(dt), showId=T, alpha=1, lwd=1, col=1, debug="draw", collapseTranscripts=F) plotTracks(dt, col=1, shape=c("smallArrow", "arrow")) plotTracks(list(GenomeAxisTrack(), dt), transcriptAnnotation="symbol", fill="#FFD58A", just.group="below", extend.left=-0.9) ## This is broken: plotTracks(list(GenomeAxisTrack(), dt), fill="#FFD58A", showId=T, just.group="below", extend.left=-0.99, extend.right=-0.99) st <- c(2000000, 2070000, 2100000, 2160000) ed <- c(2050000, 2130000, 2150000, 2170000) str <- c("-", "+", "-", "-") gr <- c("Group1","Group2","Group1", "Group3") annTrack <- AnnotationTrack(start=st, end=ed, strand=str, chromosome=7, genome="hg19", feature="test", group=gr, id=paste("annTrack item", 1:4), name="generic annotation", stacking="squish") plotTracks(annTrack)