spatialLayout {arrayMagic} | R Documentation |
All value
s 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 value
s.
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)