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Last data update: 2014.03.03

R: Plot bead locations

plotBeadLocations

R Documentation

Plot bead locations

Description

Can plot where specified beads, or bead types were located on the array surface

Usage

plotBeadLocations(BLData, ProbeIDs = NULL, BeadIDs = NULL, array = 1, SAM = FALSE, xCol = "GrnX", yCol = "GrnY", xlab = "x-coordinate", ylab = "y-coordinate", horizontal = TRUE, main = paste("Bead", ProbeIDs, "locations"), ...)

Arguments

`BLData`	a `beadLevelData` object
`ProbeIDs`	a list of ArrayAddress IDs to plot
`BeadIDs`	a list of beads (rows in the beadLevelData object) to plot
`array`	the number of the section to plot
`SAM`	if TRUE the array is treated as a Sentrix Array Matrix (hexagonal)
`xCol`	column name for the x coordinates
`yCol`	column name for the x coordinates
`xlab`	optional label for the x axis
`ylab`	optional label for the y axis
`horizontal`	if TRUE the longest edge of the array surface will be plotted on the x axis
`main`	an optional title for the plot
`...`	any arguments to be passed to plots

Value

plot to current graphical device

Author(s)

Mark Dunning

Examples


if(require(beadarrayExampleData)){

data(exampleBLData)

##Plot location of first 100 beads as they are listed in beadLevelData object

plotBeadLocations(exampleBLData, BeadIDs = 1:100, array=1, horizontal = FALSE)



}

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
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(beadarray)
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: Biobase
Welcome to Bioconductor

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

Loading required package: ggplot2
Welcome to beadarray version 2.22.2
beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/beadarray/plotBeadLocations.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotBeadLocations
> ### Title: Plot bead locations
> ### Aliases: plotBeadLocations
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> 
> if(require(beadarrayExampleData)){
+ 
+ data(exampleBLData)
+ 
+ ##Plot location of first 100 beads as they are listed in beadLevelData object
+ 
+ plotBeadLocations(exampleBLData, BeadIDs = 1:100, array=1, horizontal = FALSE)
+ 
+ 
+ 
+ }
Loading required package: beadarrayExampleData
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>