| plotErrorBars {puma} | R Documentation |
This produces plots of probesets of interest.
plotErrorBars(
eset
, probesets = if(dim(exprs(eset))[1] <= 12) 1:dim(exprs(eset))[1] else 1
, arrays = 1:dim(pData(eset))[1] # default is to use all
, xlab = paste(colnames(pData(eset))[1:numOfFactorsToUse(eset)], collapse=":")
, ylab = "Expression Estimate"
, xLabels = apply(
as.matrix(pData(eset)[arrays,1:numOfFactorsToUse(eset)])
, 1
, function(mat){paste(mat, collapse=":")}
)
, ylim = NA
, numOfSEs = qnorm(0.975)
, globalYlim = FALSE # Not yet implemented!
, plot_cols = NA
, plot_rows = NA
, featureNames = NA
, showGeneNames = TRUE
, showErrorBars = if(
length(assayDataElement(eset,"se.exprs"))==0 ||
length(assayDataElement(eset,"se.exprs")) == sum(is.na(assayDataElement(eset,"se.exprs")))
) FALSE else TRUE
, plotColours = FALSE
, log.it = if(max(exprs(eset)) > 32) TRUE else FALSE
, eset_comb = NULL
, jitterWidth = NA
, qtpcrData = NULL
, ...
)
eset |
An object of class ExpressionSet. This is the main object being plotted. |
probesets |
A vector of integers indicating the probesets to be plotted. These integers refer to the row numbers of the eset. |
arrays |
A vector of integers indicating the arrays to be shown on plots. |
xlab |
Character string of title to appear on x-axis |
ylab |
Character string of title to appear on y-axis |
xLabels |
Vector of strings for labels of individual points on x-axis. |
ylim |
2-element numeric vector showing minimum and maximum values for y-axis. |
numOfSEs |
Numeric indicating the scaling for the error bars. The default value give error bars that include 95% of expected values. |
globalYlim |
Not yet implemented! |
plot_cols |
Integer specifying number of columns for multi-figure plot. |
plot_rows |
Integer specifying number of rows for multi-figure plot. |
featureNames |
A vector of strings for featureNames (Affy IDs). This is an alternative (to the probesets argument) way of specifying probe sets. |
showGeneNames |
Boolean indicating whether to use Affy IDs as titles for each plot. |
showErrorBars |
Boolean indicating whether error bars should be shown on plots. |
plotColours |
A vector of colours to plot. |
log.it |
Boolean indicating whether expression values should be logged. |
eset_comb |
An object of class ExpressionSet. This is a secondary object to be plotted on the same charts as eset. This should be an object created using pumaComb which holds the values created by combining information from the replicates of each condition. |
jitterWidth |
Numeric indicating the x-axis distance between replicates of the same condition. |
qtpcrData |
A 2-column matrix of qRT-PCR values (or other data to be plotted on the same charts). |
... |
Additional arguments to be passed to plot. |
This function has no return value. The output is the plot created.
Richard D. Pearson
data(affybatch.example)
varLabels(affybatch.example) <- c("level")
pData(affybatch.example) <- data.frame("level"=c("twenty","twenty","ten")
, "batch"=c("A","B","A"), row.names=rownames(pData(affybatch.example)))
eset_mmgmos <- mmgmos(affybatch.example)
plotErrorBars(eset_mmgmos)
plotErrorBars(eset_mmgmos,1:6)