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Last data update: 2014.03.03

R: PLOT CONTROL WELLS IN RTCA DATA

controlView

R Documentation

PLOT CONTROL WELLS IN RTCA DATA

Description

A convenience function to plot sample wells with control wells on an E-plate in RTCA system. To use the function the phenoData field of the RTCA object must contain a field named “GeneSymbol”.

Usage

controlView(rtca, genesymbol = c("Allstar", "COPB2", "GFP", "mock", "PLK1", "WEE1"), cols, ylim, smooth = FALSE, group = TRUE, ylab = "Normalized cell index", xlab = "Time interval (hour)", drawsd = TRUE, normline = TRUE, ncol = 1, legendpos = "topleft", pData.column="GeneSymbol",...)

Arguments

`rtca`	An object of `RTCA`.To use the function, the phenoData must contain a column which name is specified by the `pData.column` parameter.
`genesymbol`	character, gene symbols to be plotted.
`cols`	character, colors used by the provided gene symbols
`ylim`	y-axis lim
`smooth`	logical, whether the `RTCA` object should be smoothed before plotting
`group`	logical. If ‘group’ is set to `TRUE`, wells with the same GeneSymbol will be summarized and plotted. For instance, these could be biological replicates. Otherwise each well is plotted separatedly
`ylab`	y axis label
`xlab`	x axis label
`drawsd`	logical, should the error bar be drawn to represent standard deviation?
`normline`	logical, should the base-time indicated by a line? See `ratioTransform` for the concept of the base-time
`ncol`	integer, legend column number
`legendpos`	character, legend position
`pData.column`	The column which the `genesymbol` parameter will be matched with
`...`	other parameters passed to the `plot` function

Details

The function is often called to draw sample and control in one plot.

Value

NULL, the function is called for its side effect

Author(s)

Jitao David Zhang jitao_david.zhang@roche.com

Examples

require(RTCA)
  
ofile <- system.file("extdata/testOutput.csv", package="RTCA")
pfile <- system.file("extdata/testOutputPhenoData.csv", package="RTCA")

pData <- read.csv(pfile, sep="\t", row.names="Well")
metaData <- data.frame(labelDescription=c(
"Rack number",
"siRNA catalogue number",
"siRNA gene symbol",
"siRNA EntrezGene ID",
"siRNA targeting accession"
))

phData <- new("AnnotatedDataFrame", data=pData, varMetadata=metaData)
x <- parseRTCA(ofile, phenoData=phData)

controlView(x, genesymbol=c("mock","COPB2","PLK1"),ylim=c(0,2))

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)

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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(RTCA)
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: RColorBrewer
Loading required package: gtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RTCA/controlView.Rd_%03d_medium.png", width=480, height=480)
> ### Name: controlView
> ### Title: PLOT CONTROL WELLS IN RTCA DATA
> ### Aliases: controlView
> ### Keywords: hplot
> 
> ### ** Examples
> 
> require(RTCA)
>   
> ofile <- system.file("extdata/testOutput.csv", package="RTCA")
> pfile <- system.file("extdata/testOutputPhenoData.csv", package="RTCA")
> 
> pData <- read.csv(pfile, sep="\t", row.names="Well")
> metaData <- data.frame(labelDescription=c(
+ "Rack number",
+ "siRNA catalogue number",
+ "siRNA gene symbol",
+ "siRNA EntrezGene ID",
+ "siRNA targeting accession"
+ ))
> 
> phData <- new("AnnotatedDataFrame", data=pData, varMetadata=metaData)
> x <- parseRTCA(ofile, phenoData=phData)
Read 245 items
> 
> controlView(x, genesymbol=c("mock","COPB2","PLK1"),ylim=c(0,2))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>