Collapsing LOD interval and labels

[kraltendorf]

The QTL intervals and labels from my "qtldf" are collapsing on one another making them illegible (see attached). Do you have any work arounds?
troubleshooting.pdf

[kraltendorf]

Troubleshooting linkagemapview overlapping qtl intervals

Found a "brute force" work around to this problem and wanted to share
Special thanks to @neyhartj

Follow the script below to reproduce the problem and demonstrate a solution

#install packages
install.packages("LinkageMapView")
library("LinkageMapView")

#create a dataframe to test
set.seed(152)
pos <- rnorm(150, mean = 50, sd = 15)
linkage_dat <- data.frame(group = c(rep(1, 150)), position = pos, locus = paste("S_", 1:150, sep = ""))

#create a qtldf
qtldf <- data.frame(chr = rep(1, 3), qtl = c("seed_size", "seed_weight", "seed_area"), so = c(26, 27, 60), si = c(26, 27, 60),
ei = c(27, 28, 75), eo = c(27, 28, 75), col = c("black", "gray", "black"))

#it seems to only occur when the intervals begin and end close to one another

#set directory
dir <- c("/users/yourname/desktop")
setwd(dir)

#outfile
outfile = file.path(dir, "lg_test.pdf")

#this is the function that produces the figure
lmv.linkage.plot(mapthis = linkage_dat, # data
outfile = outfile, # file to output
mapthese=c(1), # which LG of those in the dataframe to map
lcol="black",lcex=2,lfont=1, # some options for color; font size; etc.
rcol="black",rcex=2,rfont=1,
showonly=c("S_150", "S_1"), # which loci to show
pdf.height=6, # pdf options
pdf.pointsize=7,
qtldf = qtldf, # datframe of qtl intervals
par(lwd=0.1), lty.axis=0)

when you add a "showonly" locus to the problem area, it will force the labels out to the right
the problem area is around 26 cM

#append a new fake locus onto the dataframe
linkage_dat_append <- data.frame(group = 1, position = 26, locus = "w")
linkage_dat1 <- rbind(linkage_dat, linkage_dat_append)

#produce a new figure
outfile = file.path(dir, "lg_test2.pdf")
lmv.linkage.plot(mapthis = linkage_dat1,
outfile = outfile,
mapthese=c(1),
lcol="black",lcex=2,lfont=1,
rcol="black",rcex=2,rfont=1,
showonly=c("S_150", "S_1", "w"), # add the fake locus to "show only"
pdf.height=6,
pdf.pointsize=7,
qtldf = qtldf,
par(lwd=0.1), lty.axis=0)

you can see that it pops the overlapping lables out to the right
you change their font to white so they are not visible

format_list <- list()

label_adjuster <- c("w")
cex <- c(0.25) #size - make it small
font <- c(1)
col <- c("white") # and white
format_list[[1]] <- list(locus = label_adjuster, font = font, cex = cex, col = col)

#produce a new figure
outfile = file.path(dir, "lg_test3.pdf")

lmv.linkage.plot(mapthis = linkage_dat1,
outfile = outfile,
mapthese=c(1),
lcol="black",lcex=2,lfont=1,
rcol="black",rcex=2,rfont=1,
showonly=c("S_150", "S_1", "w"), # add the fake locus to "show only"
pdf.height=6,
pdf.pointsize=7,
qtldf = qtldf,
par(lwd=0.1), lty.axis=0,
markerformatlist=format_list) # add a markerformatlist