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## Ligia P. Bras (Sept 2006)
## Function that shows the row and column effects (calculated by the Bscore method or the spatial normalization methods) for a given range of plates ('plates'), and in a given channel ('channel').
## The spatial offsets within the selected channel 'channel' are transformed by subtracting their minimum value, and dividing by their amplitude (max - min values), in order to confine them to the range [0,1].
plotSpatialEffects = function(object, channel=1, plates) {
if(!inherits(object, "cellHTS")) stop("'object' should be of class 'cellHTS'.")
rowcol <- plateEffects(object)[["rowcol"]]
d <- dim(Data(object))
nrReplicates <- d[2]
nrPlates <- max(plate(object))
## Check if rowcol.effects are not empty in the 'cellHTS' object
if(length(rowcol)==0)
stop("No information in slot 'rowcol.effects'! Please normalize 'object' using 'normalizePlates' with parameter 'method' = 'Bscore' or 'loess' or 'locfit', and 'save.model=TRUE'.")
if(channel > dim(rowcol)[3])
stop("Choose a correct channel number using argument 'channel'!")
if (missing(plates)) {
plates = 1:nrPlates
} else {
if(!is(plates, "vector") | !all(plates %in% 1:nrPlates))
stop(sprintf("\n 'plates' should be a vector of integers between 1 and %s giving the ID number of the plates to display.", nrPlates))
}
myMax = function(x) {
x = x[!is.na(x)]
ifelse(length(x)>=1, max(x), as.numeric(NA))
}
myMin = function(x) {
x = x[!is.na(x)]
ifelse(length(x)>=1, min(x), as.numeric(NA))
}
nPlates = length(plates)
pushViewport(viewport(layout = grid.layout(nrReplicates, nPlates)))
selx = array(rowcol[,,channel], dim=c(prod(pdim(object)), nrPlates, nrReplicates))
# set range of sel to [0,1]
selx = (selx-myMin(selx))/(myMax(selx)-myMin(selx))
for (r in 1:nrReplicates)
for (p in 1:nPlates) {
wp = plates[p]
#xrange = range(aux, na.rm=TRUE)
sel = selx[,wp,r]
pushViewport(viewport(layout.pos.row=r, layout.pos.col=p))
plotPlate(as.numeric(t(sel)), nrow=pdim(object)["nrow"], ncol=pdim(object)["ncol"], na.action="xout",main=sprintf("Row + Column offsets, Plate %d, Replicate %d, Channel %s",wp, r, channel), col=rev(brewer.pal(9, "RdBu")), cex.main=0.8, cex.lab=1.1, add=TRUE, xrange=c(0,1))
popViewport()
}
popViewport()
}
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