polymapR (version 1.1.1)

check_map: 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,
  sortmarkers = TRUE,
  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.

sortmarkers

If TRUE (by default) the markers in the linkage_list are sorted: first the lower position, then the higher. Results in an averaging (in plot B) over all markers at a gives pair of positions

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)
# }