An R package to visualize genetic maps.
So far, gmap is only available on GitHub because it is still in development stage.
# use devtools to install the development version
library(devtools)
devtools::install_github("mschemmel/gmap")# load package
library(gmap)
# import genetic map
# ------------------------------
# marker | linkage group | cM
# ------------------------------
# marker1 | lg01 | 0
# marker2 | lg01 | 0.4
# marker3 | lg01 | 0.8
# ... | ... | ...
linmap <- read.map("inst/extdata/map.txt")
# store IDs of linkage groups to plot
linkagegroup <- c("lg0", "lg1", "lg2", "lg3", "lg4")
# minimal example
# plot genetic map with requested linkage groups
genmap(linmap, linkagegroup)For more detailed information see the wiki (in planning).
genmap(linmap,
linkagegroup,
title = "Organism",
marker.color = "aquamarine3",
show.marker.count = TRUE,
marker.count.color = "gray50",
show.axis = TRUE)
genmap(linmap,
linkagegroup,
title = "Organism",
marker.color = "aquamarine3",
show.marker.count = TRUE,
marker.count.color = "gray50",
show.axis = TRUE,
label.chr = c(1:12),
highlight.marker = list(firebrick = c("marker150", "marker222","marker250", "marker251"),
gold = c("marker89", "marker100"),
brown = linmap$marker[800:810],
red = linmap$marker[1100:1110]))
