compare_maps {polymapR}

Compare linkage maps, showing links between connecting markers common to neighbouring maps

Description

This function allows the visualisation of connections between different maps, showing them side by side.

Usage

compare_maps(
  maplist,
  chm.wd = 0.2,
  bg.col = "white",
  links.col = "grey42",
  thin.links = NULL,
  type = "karyotype",
  ...
)

Arguments

maplist

A list of maps. This is probably most conveniently built on-the-fly in the function call itself. If names are assigned to different maps (list items) these will appear above the maps. In cases of multiple comparisons, for example comparing 1 map of interest to 3 others, the map of interest can be supplied multiple times in the list, interspersed between the other maps. See the example below for details.

chm.wd

The width in inches that linkage groups should be drawn. By default 0.2 inches is used.

bg.col

The background colour of the maps, by default white. It can be useful to use a different background colour for the maps. In this case, supply bg.col as a vector of colour identifiers, with the same length as maplist and corresponding to its elements in the same order. See the example below for details.

links.col

The colour with which links between maps are drawn, by default grey.

thin.links

Option to thin the plotting of links between maps, which might be useful if there are very many shared markers in a small genetic region. By default NULL, otherwise supply a value (in cM) for the minimum genetic distance between linking-lines (e.g. 0.5).

type

Plot type, by default "karyotype". If "scatter" is requested a scatter plot is drawn, but only if the comparison is between 2 maps.

...

option to supply arguments to the plot function (e.g. main = to add a title to the plot)

Value

NULL

Examples

data("map1","map2","map3")
compare_maps(maplist=list("1a"=map1,"c08"=map2,"1b"=map3),bg.col=c("thistle","white","skyblue"))