## ----include=FALSE------------------------------------------------------------ library(knitr) opts_chunk$set(tidy=FALSE) ## ----loading-package, message=FALSE------------------------------------------- library(Pviz) ## ----ATrack-example, fig.height=1.5------------------------------------------- at<-ATrack(start = c(250, 480), end = c(320, 520), id = c("Anno1", "Anno2"), showFeatureId = TRUE, fontcolor = "black", name = "Annotations") plotTracks(at, from = 1, to = 600) ## ----DTrack-example, fig.height=4--------------------------------------------- library(pepDat) data(restab_aggregate) dt <- DTrack(data = restab_aggregate$group2, start = restab_aggregate$start, width=15, name="Freq", type = "l") plotTracks(dt, from = 1, to = 850, type = "l") ## ----ProteinAxisTrack-basic, fig.height=1.1----------------------------------- pat<-ProteinAxisTrack() plotTracks(pat, from = 1, to = 850) ## ----ProteinAxisTrack-options, fig.height=1.1--------------------------------- pat<-ProteinAxisTrack(addNC = TRUE, littleTicks = TRUE) plotTracks(pat, from = 1, to = 850) ## ----ProteinSequenceTrack-basic, fig.height=1.5------------------------------- data(pep_hxb2) hxb2_seq <- metadata(pep_hxb2)$sequence st <- ProteinSequenceTrack(sequence = hxb2_seq, name = "env") plotTracks(trackList = c(pat, st), from = 1, to = 40) ## ----ProteinSequenceTrack-unreadable, fig.height=1.5-------------------------- st <- ProteinSequenceTrack(sequence = hxb2_seq, name = "env", cex = 0.5) plotTracks(trackList = c(pat, st), from = 1, to = 850) ## ----ProbeTrack-basic, fig.width=9, fig.height=4.5---------------------------- data(restab) pt<-ProbeTrack(sequence = restab$peptide, intensity = restab$group2, probeStart = restab$start) plotTracks(pt, from = 460, to = 560) ## ----ProbeTrack-wide-ranges, fig.width=9, fig.height=4.5---------------------- plotTracks(pt, legend = TRUE) ## ----CladeTrack, fig.width=9, fig.height=4------------------------------------ ctA <- CladeTrack(restab, clade = "A", type = "l") ctM <- CladeTrack(restab, clade = "M", type = "l", legend = TRUE) plotTracks(c(ctA, ctM), main = "Clades comparison", cex.main = 1.5) ## ----complex-plot, fig.width=9, fig.height=6---------------------------------- pt <- ProbeTrack(sequence = restab$peptide, intensity = restab$group2, probeStart = restab$start, cex=0, legend=TRUE) plotTracks(trackList=c(pat, st, at, pt, ctM), from=460, to=560, type="l") ## ----plot-inter, fig.width=9, fig.height=4------------------------------------ plot_inter(restab_aggregate) ## ----plot-clade, fig.width=9, fig.height=4------------------------------------ plot_clade(restab, clade = c("A", "B", "C"), sequence = hxb2_seq, from = 100, to = 600) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()