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Added options for density map #8

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Added options for density map #8

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6e8bd7f
Added options for density map
IdoBar Nov 29, 2018
1c6b560
Update lmv.linkage.plot.R
IdoBar Nov 29, 2018
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24 changes: 20 additions & 4 deletions R/lmv.linkage.plot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,12 @@
#' @param col.main The color to be used for the main title.
#' Defaults to par("col.main").
#'
#' @param cex.dens The magnification to be used for density map axis text.
#' Defaults to 0.75*(par("cex.axis")).
#'
#' @param inverse.dens Optionally inverse the density map labels (Loci/cM).
#' Defaults to TRUE.
#'
#' @param conndf An optional data frame containing markers to be connected
#' with lines (homologs). If autoconnadj = TRUE, these lines will
#' appear as well as those with the same name in adjacent linkage
Expand Down Expand Up @@ -424,6 +430,8 @@ lmv.linkage.plot <- function(mapthis,
col.axis = par("col.axis"),
col.lgtitle = par("col.main"),
col.main = par("col.main"),
cex.dens=0.75*(par("cex.axis")),
inverse.dens=TRUE,
conndf = NULL,
denmap = FALSE,
dupnbr = FALSE,
Expand Down Expand Up @@ -1403,17 +1411,25 @@ lmv.linkage.plot <- function(mapthis,
bplotdens <- append(bplotdens, uleg$dens[length(uleg$dens)])
bplotcol <- append(bplotcol, uleg$col[length(uleg$col)])
}

if (inverse.dens) {
dens_label <- sprintf("Density (Loci/%s)", units)
dens_labs <- round(1/bplotdens, 1)
} else {
dens_label <- sprintf("Density (%s/Loci)", units)
dens_labs <- bplotdens
}
par(mar = c(5, leftmar, 1, 1))
barplot(
rep(1, length(bplotcol)),
col = bplotcol,
space = 0,
axes = F,
xlab = paste("Density (", units, "/Locus)", sep = ""),
names = bplotdens,
cex.names = .75,
xlab = dens_label,
names = dens_labs,
cex.names = cex.dens,
las = 2,
cex.lab = .75
cex.lab = cex.dens
)

}
Expand Down