plotChip {HELP} | R Documentation |
Graphic display of spatially-linked data, particularly applicable for microarrays
plotChip(x, y, z, ...)
x |
vector of numerical data determining x-coordinates of data on chip. x can also handle ExpressionSet (see plotChip-methods for more parameter details). |
y |
vector of numerical data determining y-coordinates of data on chip |
z |
the vector of numerical data to be plotted |
... |
Arguments to be passed to methods (see plotChip-methods ):
element AssayData to use for a given ExpressionSet input (default is "exprs") 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.x featureData to use as X coordinate (default is "X" ). Can be a character matching varLabel or simply an integer indicating which feature to choose. feature.y featureData to use as Y coordinate (default is "Y" ). Can be a character matching varLabel or simply an integer indicating which feature to choose. na.rm x , y , and z . If FALSE (default) any missing values cause an error. main title . xlab title . ylab title . colors rev(rainbow(n=20, start=0, end=1/3)) ). Also determines the resolution of z such that the more colors that are used allow finer discrimination of differences in z . range c(NA, NA) ) specifying range used to color-code data in z nrows ncols ... plot . See plot . |
Reid F. Thompson (rthompso@aecom.yu.edu), Mark Reimers (mreimers@vcu.edu)
#demo(pipeline,package="HELP") x <- rep(1:100,100) y <- rep(1:100,each=100) z <- x*(1001:11000/1000) z <- z-mean(z) z <- z*(sample(1:10000/10000)+1) plotChip(x,y,z,main="Curved gradient",xlab="x",ylab="y") plotChip(x,y,sample(1:10000,size=10000),colors=gray(0:50/50),range=c(1,10000),main="Random noise") #rm(x,y,z)