README.md

gmap-modified

An R package to visualize genetic maps. A fork.

Modifications

Modified to use csv style inputs and physical map rather than cM (genetic map).

Installation

Development version

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("vargasrichards/gmap-modified")

Usage

# 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).

Examples

genmap(linmap,
       linkagegroup, 
       title = "Organism", 
       marker.color = "aquamarine3",
       show.marker.count = TRUE,
       marker.count.color = "gray50",
       show.axis = TRUE)

Add highlighting and annotation label

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]))