controlView: PLOT CONTROL WELLS IN RTCA DATA

In RTCA: Open-source toolkit to analyse data from xCELLigence System (RTCA)

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 [e-mail]

See Also

RTCA

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))

RTCA documentation built on Nov. 8, 2020, 7:52 p.m.