| 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.xAssayData to use (for signal channel 1) for a given ExpressionSet input (default is "exprs") element.yAssayData to use (for signal channel 2) for a given ExpressionSet input (default is "exprs2") samplesampleNames to use as data (default is 1). Can be a character matching a sample name or simply an integer indicating which sample to choose. featurefeatureData to use as plotting feature (default is 1). Can be a character matching varLabel or simply an integer indicating which feature to choose. feature.randomfeatureData 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.randomfeatureData. random.flagfeature.random from featureData. Default is "RAND". na.rmx. If FALSE any missing values cause an error.limitcutoffcutoff2maintitle. xlabtitle. ylabtitle. ylab2title. 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)