draw_map_shiny: Draws linkage map, parents haplotypes and marker doses...

In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

Draws linkage map, parents haplotypes and marker doses Adapted from MAPpoly

Description

Draws linkage map, parents haplotypes and marker doses Adapted from MAPpoly

Usage

draw_map_shiny(
  left.lim = 0,
  right.lim = 5,
  ch = 1,
  maps.dist,
  ph.p1,
  ph.p2,
  d.p1,
  d.p2,
  snp.names = TRUE,
  software = NULL
)

Arguments

left.lim	covered window in the linkage map start position
right.lim	covered window in the linkage map end position
ch	linkage group ID
ph.p1	list containing a data.frame for each group with parent 1 estimated phases. The data.frame contain the columns: 1) Character vector with chromosome ID; 2) Character vector with marker ID; 3 to (ploidy number)*2 columns with each parents haplotypes
ph.p2	list containing a data.frame for each group with parent 2 estimated phases. See ph.p1 parameter description.
d.p1	list containing a data.frame for each group with parent 1 dosages. The data.frame contain the columns: 1) character vector with chromosomes ID; 2) Character vector with markers ID; 3) Character vector with parent ID; 4) numerical vector with dosage
d.p2	list containing a data.frame for each group with parent 2 dosages. See d.p1 parameter description
snp.names	logical TRUE/FALSE. If TRUE it includes the marker names in the plot
software	character defined from each software it comes from
maps	list containing a vector for each linkage group markers with marker positions (named with marker names)

Value

graphic representing selected section of a linkage group

viewpoly documentation built on May 29, 2024, 1:26 a.m.