Nothing
genoClusterPlotByBatch <- function(intenData,
genoData,
plot.type=c("RTheta","XY"),
snpID,
batchVar,
main.txt = NULL,
scan.sel = NULL,
colors = c("default", "neon", "primary"),
verbose = TRUE,
...)
{
if (verbose) message(paste("start time =", Sys.time()))
colors <- match.arg(colors)
# check that dimensions of intenData and genoData are equal
intenSnpID <- getSnpID(intenData)
genoSnpID <- getSnpID(genoData)
if (!all(intenSnpID == genoSnpID)) stop("snp dimensions of intenData and genoData differ")
intenScanID <- getScanID(intenData)
genoScanID <- getScanID(genoData)
if (!all(intenScanID == genoScanID)) stop("scan dimensions of intenData and genoData differ")
# Get snp.index corresponding to each snpID (while keeping same order as snpID and main.txt)
if(!all(is.element(snpID, intenSnpID))) {
stop("At least one selected SNP in snpID is invalid, make sure to use integer snpID")
}
nsnp <- length(snpID)
snp.index <- rep(NA,nsnp)
for(i in 1:nsnp) {
snp.index[i] <- which(is.element(intenSnpID, snpID[i]))
}
# get plot type
plot.type <- match.arg(plot.type)
# Get sample index corresponding to each scan.sel to include in plot
if(!is.null(scan.sel)) {
if(!all(is.element(scan.sel, intenScanID))) {
stop("At least one selected sample in scan.sel is not in the genotype file")
}
samp.plot <- is.element(intenScanID, scan.sel)
} else {
samp.plot <- rep(TRUE, length(intenScanID))
}
# check that batchVar is present
if (hasScanVariable(intenData, batchVar)) {
sample.ann.plates <- getScanVariable(intenData, batchVar)
} else if (hasScanVariable(genoData, batchVar)) {
sample.ann.plates <- getScanVariable(genoData, batchVar)
} else stop ("batchVar not found in intenData or genoData")
plates <- unique(sample.ann.plates[samp.plot])
np <- length(plates);
if (is.null(main.txt)) {
main.txt <- paste("snp", as.character(snpID))
}
for(i in 1:nsnp) { # loop through snp int.ids
geno <- getGenotype(genoData, snp=c(snp.index[i],1), scan=c(1,-1))
y <- getY(intenData, snp=c(snp.index[i],1), scan=c(1,-1))
x <- getX(intenData, snp=c(snp.index[i],1), scan=c(1,-1))
for(j in 1:np){ # loop through plates
cplate <- plates[j];
samp.logic1 <- sample.ann.plates == cplate
if(!is.null(scan.sel)) {
samp.logic <- samp.logic1 & samp.plot
} else { samp.logic <- samp.logic1 }
if (verbose) message(paste("i=",i,"j=",j, Sys.time()))
genosm <- geno[samp.logic];
ysm <- y[samp.logic];
xsm <- x[samp.logic];
stopifnot(length(genosm)==length(ysm) & length(ysm)==length(xsm))
xcol <- rep(NA, length(genosm))
cols <- .colorByGeno(colors)
xcol[is.na(genosm)] <- cols["NA"]
xcol[genosm==0] <- cols["BB"]
xcol[genosm==1] <- cols["AB"]
xcol[genosm==2] <- cols["AA"]
stopifnot(sum(is.na(xcol))==0)
xpch <- rep(NA, length(genosm))
xpch[is.na(genosm)] <- 4
xpch[!is.na(genosm)] <- 1
stopifnot(sum(is.na(xpch))==0)
txt <- paste(main.txt[i], "\n", as.character(cplate), sep="")
if(plot.type=="RTheta") {
theta <- atan(ysm/xsm)*(2/pi)
r <- xsm+ysm
plot(theta, r, xlab="Theta", ylab="R", xlim=c(0,1),col=xcol, pch=xpch, main=txt, cex=0.8, ...)
} else {
plot(xsm, ysm, xlab="X", ylab="Y",col=xcol, pch=xpch, main=txt, cex=0.8, ...)
}
rm(genosm); rm(xsm); rm(ysm)
} #j
} #i
}
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