plotFeature {HELP} | R Documentation |
Graphical display of featureData (ex: fragment size) versus two-color signal intensity data
plotFeature(x, y, ...)
x |
matrix of numerical data to be plotted, with two columns (one for each signal channel). x can also be of class "ExpressionSet" . |
y |
an additional vector of numerical data to be used for feature. If y is missing, the function will attempt to fill a value from featureData in x . |
... |
Arguments to be passed to methods (see plotFeature-methods ):
element.x AssayData to use (for signal channel 1) for a given ExpressionSet input (default is "exprs") element.y AssayData to use (for signal channel 2) for a given ExpressionSet input (default is "exprs2") sample sampleNames to use as data (default is 1). Can be a character matching a sample name or simply an integer indicating which sample to choose. feature featureData to use as plotting feature (default is 1). Can be a character matching varLabel or simply an integer indicating which feature to choose. feature.random featureData to use to identify random probes (default is "TYPE"). Can be a character matching varLabel or simply an integer indicating which feature to choose. which.random featureData . random.flag feature.random from featureData . Default is "RAND". na.rm x . If FALSE any missing values cause an error.limit cutoff cutoff2 main title . xlab title . ylab title . ylab2 title . cex ... plot . See plot . |
Reid F. Thompson (rthompso@aecom.yu.edu)
#demo(pipeline,package="HELP") msp1 <- sample(8000:16000/1000, size=1000) msp1 <- msp1[order(msp1)] hpa2 <- sample(8000:16000/1000, size=1000) hpa2 <- hpa2[order(hpa2)] size <- sample((1:1000)*1.8+200, size=1000) rand <- which.min(abs(msp1-quantile(msp1, 0.25))) plotFeature(cbind(msp1, hpa2), size, which.random=(rand-20):(rand+20), main="Random") #rm(msp1, hpa2, size, rand)