plotChip: Plot chip image

In HELP: Tools for HELP data analysis

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 [e-mail], Mark Reimers [e-mail]

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)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

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    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

HELP documentation built on Nov. 8, 2020, 11:08 p.m.