drawFeatures {BubbleTree} | R Documentation |
draw the features
drawFeatures(.Object, rbd, col = NULL) ## S4 method for signature 'BTreePlotter' drawFeatures(.Object, rbd, col = "black")
.Object |
the object |
rbd |
the rbd object |
col |
the col value |
draw the annotation on the track
load(system.file("data", "allCall.lst.RData", package="BubbleTree")) load(system.file("data", "cancer.genes.minus2.rda", package="BubbleTree")) load(system.file("data", "vol.genes.rda", package="BubbleTree")) load(system.file("data", "gene.uni.clean.gr.rda", package="BubbleTree")) load(system.file("data", "cyto.gr.rda", package="BubbleTree")) # 77 common cancer genes merged from 2 sets comm <- btcompare(vol.genes, cancer.genes.minus2) btreeplotter <- new("BTreePlotter", branch.col="gray50") annotator <- new("Annotate") nn <- "sam12" cc <- allCall.lst[[nn]] z <- drawBTree(btreeplotter, cc@rbd.adj) + ggplot2::labs(title=sprintf("%s (%s)", nn, info(cc))) out <- cc@result$dist %>% filter(seg.size >= 0.1 ) %>% arrange(gtools::mixedorder(as.character(seqnames)), start) ann <- with(out, { annoByGenesAndCyto(annotator, as.character(out$seqnames), as.numeric(out$start), as.numeric(out$end), comm$comm, gene.uni.clean.gr=gene.uni.clean.gr, cyto.gr=cyto.gr) }) out$cyto <- ann$cyto out$genes <- ann$ann v <- z + drawFeatures(btreeplotter, out) print(v)