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Last data update: 2014.03.03

R: Plot SNP data and/or aspcf segmentation results

plotAllele

R Documentation

Plot SNP data and/or aspcf segmentation results

Description

Plot bivariate SNP data and/or aspcf segmentation results for each sample separately with chromosomes in different panels

Usage

plotAllele(logR = NULL, BAF = NULL, segments = NULL, pos.unit = "bp", 
            sample = NULL, chrom = NULL, assembly="hg19", baf.thres = 
            c(0.1,0.9), winsoutliers = NULL, xaxis = "pos", layout = c(1,1), 
            plot.ideo = TRUE, ...)

Arguments

`logR`	a data frame with numeric or character chromosome numbers in the first column, numeric local probe positions in the second, and numeric copy number data for one or more samples in subsequent columns. The header of the copy number column(s) should give the sample IDss.
`BAF`	a data frame on the same format and size as `logR`, with chromosomes and local probe positions in the two first columns, and numeric BAF-measurements for one or more samples in subsequent columns.
`segments`	a data frame or a list of data frames containing the segmentation results found by `aspcf`.
`pos.unit`	the unit used to represent the probe positions. Allowed options are "mbp" (mega base pairs), "kbp" (kilo base pairs) or "bp" (base pairs). By default assumed to be "bp".
`sample`	a numeric vector indicating which sample(s) is (are) to be plotted. The number(s) should correspond to the sample's place (in order of appearance) in `logR`, or in `segments` if `logR` is unspecified.
`chrom`	a numeric or character vector with chromosome number(s) to indicate which chromosome(s) is (are) to be plotted.
`assembly`	a string specifying which genome assembly version should be applied to define the chromosome ideogram. Allowed options are "hg19", "hg18", "hg17" and "hg16" (corresponding to the four latest human genome annotations in the UCSC genome browser).
`baf.thres`	a numeric vector of length 2 giving thresholds below/above which BAF-values will not be plotted (use this to remove germline homozygous BAF probes from the plot).
`winsoutliers`	an optional data frame of the same size as `logR` identifying observations classified as outliers by `winsorize`. If specified, outliers will be marked by a different color and symbol than the other observations (see `wins.col` and `wins.pch`).
`xaxis`	either "pos" or "index". The former implies that the xaxis will represent the genomic positions, whereas the latter implies that the xaxis will represent the probe indices. Default is "pos".
`layout`	an integer vector of length two giving the number of rows and columns in the plot. Default is `c(1,1)`.
`plot.ideo`	a logical value indicating whether the chromosome ideogram should be plotted. Only applicable when `xaxis="pos"`.
`...`	other graphical parameters. These include the common plot arguments `xlab`, `ylab`, `main`, `xlim`, `ylim`, `col` (default is "grey"), `pch` (default is 46, equivalent to "."), `cex`, `cex.lab`, `cex.main`, `cex.axis`, `las`, `tcl`, `mar` and `mgp` (see `par` on these). In addition, a range of graphical arguments specific for copy number plots may be specified, see `plotSample` on these.

Details

Several chromosome may be displayed on the same page with the layout option. If the number of chromosomes exceeds the desired page layout, the user is prompted before advancing to the next page of output.

Note

This function applies par(fig), and is therefore not compatible with other setups for arranging multiple plots in one device such as par(mfrow,mfcol).

Author(s)

Gro Nilsen

Examples

#Load logR and BAF data:
data(logR)
data(BAF)

#Run aspcf::
aspcf.segments <- aspcf(logR,BAF)

#Plot
plotAllele(logR,BAF,aspcf.segments,layout=c(2,2))

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.

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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
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Type 'q()' to quit R.

> library(copynumber)
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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/copynumber/plotAllele.rd_%03d_medium.png", width=480, height=480)
> ### Name: plotAllele
> ### Title: Plot SNP data and/or aspcf segmentation results
> ### Aliases: plotAllele
> 
> ### ** Examples
> 
> #Load logR and BAF data:
> data(logR)
> data(BAF)
> 
> #Run aspcf::
> aspcf.segments <- aspcf(logR,BAF)
aspcf finished for chromosome arm 1p 
aspcf finished for chromosome arm 1q 
aspcf finished for chromosome arm 2p 
aspcf finished for chromosome arm 2q 
aspcf finished for chromosome arm 3p 
aspcf finished for chromosome arm 3q 
aspcf finished for chromosome arm 4p 
aspcf finished for chromosome arm 4q 
aspcf finished for chromosome arm 5p 
aspcf finished for chromosome arm 5q 
aspcf finished for chromosome arm 6p 
aspcf finished for chromosome arm 6q 
aspcf finished for chromosome arm 7p 
aspcf finished for chromosome arm 7q 
aspcf finished for chromosome arm 8p 
aspcf finished for chromosome arm 8q 
aspcf finished for chromosome arm 9p 
aspcf finished for chromosome arm 9q 
aspcf finished for chromosome arm 10p 
aspcf finished for chromosome arm 10q 
aspcf finished for chromosome arm 11p 
aspcf finished for chromosome arm 11q 
aspcf finished for chromosome arm 12p 
aspcf finished for chromosome arm 12q 
aspcf finished for chromosome arm 13q 
aspcf finished for chromosome arm 14q 
aspcf finished for chromosome arm 15q 
aspcf finished for chromosome arm 16p 
aspcf finished for chromosome arm 16q 
aspcf finished for chromosome arm 17p 
aspcf finished for chromosome arm 17q 
aspcf finished for chromosome arm 18p 
aspcf finished for chromosome arm 18q 
aspcf finished for chromosome arm 19p 
aspcf finished for chromosome arm 19q 
aspcf finished for chromosome arm 20p 
aspcf finished for chromosome arm 20q 
aspcf finished for chromosome arm 21q 
aspcf finished for chromosome arm 22q 
aspcf finished for chromosome arm Xp 
aspcf finished for chromosome arm Xq 
> 
> #Plot
> plotAllele(logR,BAF,aspcf.segments,layout=c(2,2))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>