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
# Next 4 lines commented out to save time in package checks, and saved version used # if (require(affydata)) { # data(Dilution) # eset_mmgmos <- mmgmos(Dilution) # } data(eset_mmgmos) plotErrorBars(eset_mmgmos) plotErrorBars(eset_mmgmos,1:6)