ProteinSequenceTrack

Description

A track to display peptides and protein sequences.

Usage

ProteinSequenceTrack(sequence = NULL, name = "Sequence", ...)

Arguments

Author(s)

Renan Sauteraud

See Also

SequenceTrack, DisplayPars

Examples

if(require(pepDat)){
  data(pep_hxb2)
  hxb2_seq <- metadata(pep_hxb2)$sequence
  st<-ProteinSequenceTrack(sequence=hxb2_seq, name="env")

  # Plotting amino acids
  plotTracks(st, to = 20)

  # When the range becomes wider, only coloured squares are displayed
  plotTracks(st, to = 100)

  # When overplotting, a single line will mark the ProteinSequenceTrack
  plotTracks(st)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Pviz)
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Pviz/ProteinSequenceTrack.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ProteinSequenceTrack
> ### Title: ProteinSequenceTrack
> ### Aliases: ProteinSequenceTrack ProteinSequenceTrack-class
> 
> ### ** Examples
> 
> if(require(pepDat)){
+   data(pep_hxb2)
+   hxb2_seq <- metadata(pep_hxb2)$sequence
+   st<-ProteinSequenceTrack(sequence=hxb2_seq, name="env")
+ 
+   # Plotting amino acids
+   plotTracks(st, to = 20)
+ 
+   # When the range becomes wider, only coloured squares are displayed
+   plotTracks(st, to = 100)
+ 
+   # When overplotting, a single line will mark the ProteinSequenceTrack
+   plotTracks(st)
+ }
Loading required package: pepDat
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>