polymapR (version 1.1.1)

MDSMap_from_list: Wrapper function for MDSMap to generate linkage maps from list of pairwise linkage estimates

Description

Create multidimensional scaling maps from a list of linkages

Usage

MDSMap_from_list(
  linkage_list,
  write_to_file = FALSE,
  mapdir = "mapping_files_MDSMap",
  plot_prefix = "",
  log = NULL,
  ...
)

Arguments

linkage_list

A named list with r and LOD of markers within linkage groups.

write_to_file

Should output be written to a file? By default FALSE, if TRUE then output, including plots from MDSMap are saved in the same directory as the one used for input files. These plots are currently saved as pdf images. If a different plot format is required (e.g. for publications), then run the MDSMap function estimate.map (or similar) directly and save the output with a different plotting function as wrapper around the map function call.

mapdir

Directory to which map input files are initially written. Also used for output if write_to_file=TRUE

plot_prefix

prefix for the filenames of output plots.

log

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

…

Arguments passed to estimate.map.

Examples

# NOT RUN {
data("all_linkages_list_P1")
maplist_P1 <- MDSMap_from_list(all_linkages_list_P1[1])
# }