spatialLayout {arrayMagic}R Documentation

Calculation of two dimensional coordinates

Description

All values are mapped on a matrix representing the the spatial layout defined by the function arguments, mainly by row, column and block. The result can be visualised with the function plot.imageMatrix.

Usage

spatialLayout(value, row, col, block, numberOfValues, nrOfBlocksPerRow = 4, mapping = 0, nrRow, nrCol)

Arguments

value numeric vector; required; default: missing
row integer vector; required; default: missing
col integer vector; required; default: missing
block integer vector; required; default: missing
numberOfValues integer; optional; default: missing. The argument numberOfValues may be used if not all values for all coordinates are passed to the function. An additional consistency check is offered.
nrOfBlocksPerRow integer; required; default: 4. Useful if there is a block structured layout with columns and rows assigned within each block as common for microarrays. See examples for a simple case with only one block.
mapping integer; either zero or one; default: zero, Mapping toggles between counting blocks "by row" or "by column". Zero corresponds to "ScanAlyze" and "GenePix", i.e. counting blocks "by row".
nrRow integer; optional; default: missing. The argument nrRow (number of rows per block) may be used to supersede max(row) which is calculated automatically.
nrCol integer; optional; default: missing. The argument nrCol (number of columns per block) may be used to supersede max(col) which is calculated automatically.

Value

A matrix representing the spatial layout of all values. The matrix is labelled as class imageMatrix and matrix.

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

plot.imageMatrix

Examples


 value <- rep(c(1,rep(0,49)),10)
 block <- as.integer(gl(10,50))
 col <- rep(c(1:10),50)
 row <- rep(as.integer(gl(5,10)),10)
 sL <- spatialLayout(value=value,row=row,col=col,block=block,nrOfBlocksPerRow=2)
 plot.imageMatrix(sL)
 value <- value[-(201:250)]
 block <- block[-(201:250)]
 col <- col[-(201:250)]
 row <- row[-(201:250)]
 sL <- spatialLayout(value=value,row=row,col=col,block=block,nrOfBlocksPerRow=2,numberOfValues=500)
 plot.imageMatrix(sL)

 value <- 1:200
 block <- rep(1, 200)
 col <- rep(1:20, 10)
 row <- as.integer(gl(10,20))
 sLOne <- spatialLayout(value=value,block=block,col=col,row=row,nrOfBlocksPerRow=1)
        

[Package arrayMagic version 1.10.0 Index]