ATrack class

Description

This class contains Gviz's AnnotationTrack and adds default values to the genome and chromosome slot

Usage

ATrack(range = NULL, start = NULL, end = NULL, width = NULL, group, id,
  stacking = "squish", name = "ATrack", fun, selectFun, ...)

Arguments

Author(s)

Renan Sauteraud

See Also

AnnotationTrack, GdObject

Examples

# Object construction
aTrack <- ATrack(start = c(20, 60), end = c(40, 100), name = "random.anno",
id=c("small","big"))
#Stacking example
a2Track <- ATrack(start = c(20, 30), end = c(40, 100), name = "stacking=dense",
id = c("small", "big"), stacking = "dense", fill=c("black", "orange"))
a3Track <- ATrack(start = c(20, 30), end = c(40, 100), name = "no stacking",
id = c("small", "big"), fill = c("black", "orange"))
#Plotting
plotTracks(trackList = c(aTrack, a2Track, a3Track), showFeatureId = TRUE)

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.
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Type 'license()' or 'licence()' for distribution details.

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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/ATrack.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ATrack
> ### Title: ATrack class
> ### Aliases: ATrack ATrack-class
> 
> ### ** Examples
> 
> # Object construction
> aTrack <- ATrack(start = c(20, 60), end = c(40, 100), name = "random.anno",
+ id=c("small","big"))
> #Stacking example
> a2Track <- ATrack(start = c(20, 30), end = c(40, 100), name = "stacking=dense",
+ id = c("small", "big"), stacking = "dense", fill=c("black", "orange"))
> a3Track <- ATrack(start = c(20, 30), end = c(40, 100), name = "no stacking",
+ id = c("small", "big"), fill = c("black", "orange"))
> #Plotting
> plotTracks(trackList = c(aTrack, a2Track, a3Track), showFeatureId = TRUE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>