Nothing
# Automatically connect adjacent markers.
# Create data frame of information to automatically connect markers
# of the same name on adjacent linkage groups in the same row
#
#
# Input: A list of linkage group data
#
# Returns: A data frame containing one row for every connection to
# drawn between homologs (markers of the same name on adjacent
# linkage groups).
autoconn <-
function(lg, fg, lgperrow) {
conndf <- data.frame(
fromchr = character(),
fromlocus = character(),
tochr = character(),
tolocus = character(),
col = character(),
stringsAsFactors = FALSE
)
# first remove any "(## more)" labels generated by dupnbr=TRUE
newlg <- list()
for (i in 1:length(lg)) {
morelab <- lg[[i]]$locus[grep("more)", lg[[i]]$locus)]
newlg[[i]] <-
subset(lg[[i]],!(lg[[i]]$locus %in% morelab) &
!(lg[[i]]$locus == ""))
}
# next pick out the from
if (length(newlg) > 1) {
for (i in 2:length(newlg)) {
# if no locus labels at all skip it (density map)
if (nrow(newlg[[i - 1]]) > 0 &
nrow(newlg[[i]]) > 0) {
# don't connect if for some reason they requested
# the same linkage group side by side
# or if they are going to be in different rows
if (!(newlg[[i - 1]][1, 1] == newlg[[i]][1, 1])
&& (i - 1) %% lgperrow != 0) {
connlocus <-
newlg[[i - 1]]$locus[newlg[[i - 1]]$locus %in% newlg[[i]]$locus]
if (length(connlocus) > 0) {
conndf <- rbind(
conndf,
data.frame(
fromchr = newlg[[i - 1]][1, 1],
fromlocus = connlocus,
tochr = newlg[[i]][1, 1],
tolocus = connlocus,
col = fg
)
)
}
}
}
}
}
return (conndf)
}
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