| spatialLayout {arrayMagic} | R Documentation |
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.
spatialLayout(value, row, col, block, numberOfValues, nrOfBlocksPerRow = 4, mapping = 0, nrRow, nrCol)
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. |
A matrix representing the spatial layout of all values.
The matrix is labelled as class imageMatrix and matrix.
Andreas Buness <a.buness@dkfz.de>
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)