Plot data superimposed on chromosomal ideogram

Description

Main function to plot binned data alongside chromosomal ideogram.

Usage

plotOnIdeo(chrom = stop("enter chromosome(s) to plot"), ideoTable, 
    values_GR, value_cols = "values", plotType = "lines", col = "orange", 
    bpLim = NULL, val_range = NULL, addScale = TRUE, scaleChrom = TRUE, 
    vertical = FALSE, addOnetoStart = TRUE, smoothVals = FALSE, cex.axis = 1,     plot_title = NULL, ablines_y = NULL, cex.main=1, ...)

Arguments

Details

plotOnIdeo() is the main function of this package. It is the one the end-user is expected to call to generate plots. Input is provided as a GRanges object (values_GR), with data to be plotted contained in its metadata slot. The user is responsible for providing pre-binned data, if binning is required. Data can also be binned using the avgByBin() function in this package. The ideogram table (ideoTable) is the same as the cytoBandIdeo table available from the UCSC genome browser database for a given genome is a can be either automatically downloaded from UCSC (see getIdeo()) or read in from a local-file and passed to this function.

There are numerous arguments which control the appearance of the plot. The main decision points are:

1. vertical: Whether the entire plot should have a horizontal or vertical orientation

2. plotType: Whether each dataseries should be shown as a trendline or as a barplot. The latter is not recommended for cases where multiple series are to be plotted on the same axis.

Other considerations:

• The size of the graphics device limits the number of chromosomes that can be plotted. A simple solution may be to set addScale=FALSE. However, it is recommended to call plotOnIdeo() multiple times, and plotting a fewer number of chromosomes on each page.

• The code expects coordinates of values_GR to be in 1-base. Set addOneToStart=TRUE if supplied coordinates are in 0-base.

Author(s)

Shraddha Pai <Shraddha.Pai@camh.ca>, Jingliang Ren

Examples

data(binned_multiSeries)
data(hg18_ideo)
plotOnIdeo(chrom=seqlevels(binned_multiSeries),ideoTable=hg18_ideo, values_GR=binned_multiSeries, value_cols=colnames(mcols(binned_multiSeries)), col=1:5)

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)

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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(IdeoViz)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: RColorBrewer
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IdeoViz/plotOnIdeo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotOnIdeo
> ### Title: Plot data superimposed on chromosomal ideogram
> ### Aliases: plotOnIdeo
> 
> ### ** Examples
> 
> data(binned_multiSeries)
> data(hg18_ideo)
> plotOnIdeo(chrom=seqlevels(binned_multiSeries),ideoTable=hg18_ideo, values_GR=binned_multiSeries, value_cols=colnames(mcols(binned_multiSeries)), col=1:5)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>