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 1.0.0 Index]