check_map: Check the quality of a linkage map using heatplots

In polymapR: Linkage Analysis in Outcrossing Polyploids

Check the quality of a linkage map using heatplots

Description

Perform a series of checks on a linkage map and visualise the results using heatplots. Also shows the discrepency between the pairwise and multi-point r estimates, plotted against the LOD of the pairwise estimate.

Usage

check_map(
  linkage_list,
  maplist,
  mapfn = "haldane",
  lod.thresh = 5,
  tidyplot = TRUE,
  detail = 1,
  plottype = c("", "pdf", "png")[1],
  prefix = ""
)

Arguments

linkage_list	A named list with r and LOD of markers within linkage groups.
maplist	A list of maps. In the first column marker names and in the second their position.
mapfn	The map function used in generating the maps, either one of "haldane" or "kosambi". By default "haldane" is assumed.
lod.thresh	Numeric. Threshold for the LOD values to be displayed in heatmap, by default 5 (set at 0 to display all values)
tidyplot	If TRUE, an attempt is made to reduce the plot density, using the hexbin package. This can have a considerable performance impact for high-density maps
detail	Level of detail for heatmaps, by default 1 cM. Values less than 0.5 cM can have serious performance implications.
plottype	Option to specify graphical device for plotting, (either png or pdf), or by default "", in which case plots are directly plotted within R
prefix	Optional prefix appended to plot names if outputting plots.

Examples

## Not run: 
data("maplist_P1","all_linkages_list_P1")
check_map(linkage_list = all_linkages_list_P1, maplist = maplist_P1)

## End(Not run)

polymapR documentation built on Nov. 5, 2023, 1:09 a.m.