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 ... 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 1.2.0 Index]