plotChip {HELP} | R Documentation |
Plot chip image
Description
Graphic display of spatially-linked data, particularly applicable for microarrays
Usage
plotChip(x, y, z, ...)
Arguments
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
which element of AssayData to use for a given ExpressionSet input (default is "exprs")
- sample
which element of 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
which element of 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
which element of 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
logical; if TRUE, missing values are
removed from x , y , and z . If FALSE
(default) any missing values cause an error.
- main
an overall title for the plot: see title .
- xlab
a title for the x axis: see title .
- ylab
a title for the y axis: see title .
- colors
vector of colors specifying the color scheme to
use (default is 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
vector of numerical data of length 2 (default is
c(NA, NA) ) specifying range used to color-code data in z
- nrows
numerical input specifying the number of rows by
which to divide the chip; default is NULL which skips the
division of data into blocks and results in individual spot resolution
- ncols
numerical input specifying the number of columns
by which to divide the chip; default is NULL which skips the
division of data into blocks and results in individual spot resolution
- \dots
other arguments to be passed to plot . See plot .
|
Author(s)
Reid F. Thompson rthompso@aecom.yu.edu, Mark Reimers mreimers@vcu.edu
See Also
plotChip-methods
Examples
#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)
[Package
HELP version 1.48.0
Index]