Nothing
# extract one linkage group
getlg <- function(df, lg, dupnbr,roundpos) {
# if dupnbr is true user wants only first marker name
# at a position to show with (### more) after the marker name
# to indicate how many more markers at that position
# We'll use (### more) as the second label so that the first
# label isn't corrupted for connecting homologous markers
# based on matching marker names. That means we need to
# set maxnbrcolsfordups <- 2 in lmv.linkage.plot.
templg <- subset(df, df[, 1] == lg)
# make sure linkage group is in order by position
thislg <- templg[order(templg$position),]
thislg$position <- round(thislg$position, roundpos)
if (dupnbr) {
keeprows <- vector()
dupcount <- vector(length = nrow(thislg))
keeprows <- append(keeprows, 1) # always keep first row
dupcount[1] <- 0
i <- 0
for (i in 2:nrow(thislg)) {
if (thislg$position[i] == thislg$position[i - 1]) {
dupcount[i] <- dupcount[i - 1] + 1
if (dupcount[i] == 1) {
keeprows <- append(keeprows, i) # for (## more label)
}
}
else {
if (dupcount[i - 1] > 0) {
thislg$locus[i - dupcount[i - 1]] <-
paste(" (",
dupcount[i - 1],
" more)",
sep = "")
}
keeprows <- append(keeprows, i)
dupcount[i] <- 0
}
}
# finish last row
if (dupcount[i] > 0) {
thislg$locus[i - dupcount[i - 1]] <-
paste(" (",
dupcount[i],
" more)",
sep = "")
}
retdf <- thislg[unique(keeprows), ]
}
else {
retdf <- thislg
}
return(retdf)
}
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