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Last data update: 2014.03.03

R: Plot a chromosome-value pair

plotChromValuePair

R Documentation

Plot a chromosome-value pair

Description

Base function which plots the ideogram and superimposed data for a single chromosome. plotOnIdeo() calls this function and stacks the resulting output.

Usage

plotChromValuePair(chrom, cytoTable, bpLim, vertical, values_GR, 
    val_range, col, value_cols = "values", default_margins, addScale, 
    ablines_y, smoothVals, span=0.03, verbose = FALSE, ...)

Arguments

`chrom`	(character) chromosome(s) to create ideograms for
`cytoTable`	(data.frame) loaded ideogram table. (see ideoTable argument to `plotOnIdeo()`)
`bpLim`	(numeric) (aka xlim); display only a section of the chromosome and the corresponding values
`vertical`	(logical) if TRUE, chromosomes will be plotted vertically
`values_GR`	(GenomicRanges) data to be plotted must be in metadata columns
`val_range`	(numeric) (aka ylim); y-axis scale for data series
`col`	(character) colour for series
`value_cols`	(character) column name for series to plot
`default_margins`	(numeric) page inner margins (in inches)
`addScale`	(logical) if FALSE, bp positions will be hidden
`ablines_y`	(numeric) when specified, will draw reference lines on the y-axis
`smoothVals`	(logical) when T applies loess() to each series
`span`	(numeric)`span` argument for `loess` function
`verbose`	(logical) print messages
`...`	arguments to `axis()`, `line()`, and `rect()`

Details

Plots one unit of chromosome ideogram with dataseries superimposed. Usually, the user can avoid this function and directly call plotOnIdeo(). However, this function may be used in cases where further plot customization is required.

Author(s)

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

Examples

data(hg18_ideo)
data(binned_multiSeries)
layout(matrix(1:2, byrow=TRUE,ncol=1),heights=c(2.5,1))
plotChromValuePair("chr1",hg18_ideo, 
	values_GR=binned_multiSeries,value_cols=colnames(mcols(binned_multiSeries)),plotType='lines',
	col=1:5,val_range=c(0,10),bpLim=NULL,vertical=FALSE,addScale=TRUE,ablines_y=NULL,
	smoothVals=FALSE,default_margins=c(0.5,.5,.1,.1))

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 'demo()' for some demos, 'help()' for on-line help, or
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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/plotChromValuePair.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotChromValuePair
> ### Title: Plot a chromosome-value pair
> ### Aliases: plotChromValuePair
> 
> ### ** Examples
> 
> data(hg18_ideo)
> data(binned_multiSeries)
> layout(matrix(1:2, byrow=TRUE,ncol=1),heights=c(2.5,1))
> plotChromValuePair("chr1",hg18_ideo, 
+ 	values_GR=binned_multiSeries,value_cols=colnames(mcols(binned_multiSeries)),plotType='lines',
+ 	col=1:5,val_range=c(0,10),bpLim=NULL,vertical=FALSE,addScale=TRUE,ablines_y=NULL,
+ 	smoothVals=FALSE,default_margins=c(0.5,.5,.1,.1))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>