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Last data update: 2014.03.03

R: Basic plotting function for obtained features

plotFeatures

R Documentation

Basic plotting function for obtained features

Description

This functions creates a basic plot with the features retrieved by getDasFeature or adds them to an existing plot.

Usage

    plotFeatures(df, col=NULL, col.start="start", col.end="end", col.id ="label", col.type="type", box.height=4, box.sep=2, pos.label=c("middle", "top", "bottom", "no"), new=TRUE, legend=TRUE, ...)

Arguments

`df`	`data.frame` with the features. Columns `col.start, col.end, col.id and col.type` must be present.
`col`	Vector of colors for each box in `df`. If `NULL`, automatic rainbow coloring for different types will be used.
`col.start, col.end, col.id, col.type`	Names of the columns of the data.frame from which retrieve the values
`box.height, box.sep`	Height and separation between boxes (in percentual points respect y-axis)
`pos.label`	Position of the label respect the box. If `pos.label=="no"`, labels are disabled.
`new`	Open a new graphical device. If `new=FALSE`, boxes will be added to an existing plot (so, coordinate system must be consistent).
`legend`	Add legend to the plot
`...`	Other graphical parameters passed to `plot.default`

Details

This function provides a quick way to view (non-overlapped) boxes in a new or an existing plot with the features retrieved.

Notice that boxes will can be plotted overlaping the current open graphical device, so the x-coordinates must match.

Value

(none)

Author(s)

Oscar Flores <oflores@mmb.pcb.ub.es>

Examples

    # This is UCSC Genome browser
    setDasServer(server="http://genome.ucsc.edu/cgi-bin/das")

    # Note that id now changes, we can retrieve it from getDasDsn()
    source <- "sacCer3"
    range <- GRanges(c("I"), IRanges(start=1, end=2500))
    type <- c("sgdGene")

    # We want the official genes from 'sdgGene' in the range I:1-2500
    features <- getDasFeature(source, range, type)
    print(features)

    plotFeatures(features)

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(DASiR)
Loading required package: Biostrings
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DASiR/plotFeatures.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotFeatures
> ### Title: Basic plotting function for obtained features
> ### Aliases: plotFeatures
> ### Keywords: plot
> 
> ### ** Examples
> 
>     # This is UCSC Genome browser
>     setDasServer(server="http://genome.ucsc.edu/cgi-bin/das")
DAS server for this session is: http://genome.ucsc.edu/cgi-bin/das
> 
>     # Note that id now changes, we can retrieve it from getDasDsn()
>     source <- "sacCer3"
>     range <- GRanges(c("I"), IRanges(start=1, end=2500))
>     type <- c("sgdGene")
> 
>     # We want the official genes from 'sdgGene' in the range I:1-2500
>     features <- getDasFeature(source, range, type)
Querying url: http://genome.ucsc.edu/cgi-bin/das/sacCer3/features
>     print(features)
  segment.range                    id     label    type method start  end score
1             1    YAL069W.chrI.334.0   YAL069W sgdGene          335  649     -
2             1  YAL068W-A.chrI.537.0 YAL068W-A sgdGene          538  792     -
3             1   YAL068C.chrI.1806.0   YAL068C sgdGene         1807 2169     -
4             1 YAL067W-A.chrI.2479.0 YAL067W-A sgdGene         2480 2707     -
  orientation phase                group
1           +     - Link to UCSC Browser
2           +     - Link to UCSC Browser
3           -     - Link to UCSC Browser
4           +     - Link to UCSC Browser
> 
>     plotFeatures(features)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>