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

Description Usage Arguments Value Author(s) References

Description

This function generates a brief summary table

This function plots a genetic linkage map(s)

Usage

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

map_summary(left.lim = 0, right.lim = 5, ch = 1, maps, d.p1, d.p2)

summary_maps(viewmap, verbose = TRUE)

plot_map_list(viewmap, horiz = TRUE, col = "ggstyle", title = "Linkage group")

gg_color_hue(n)

plot_one_map(x, i = 0, horiz = FALSE, col = "lightgray")

Arguments

viewmap

object of class viewmap

horiz

logical. If FALSE, the maps are plotted vertically with the first map to the left. If TRUE (default), the maps are plotted horizontally with the first at the bottom

col

a vector of colors for the bars or bar components (default = 'lightgrey') ggstyle produces maps using the default ggplot color palette

title

a title (string) for the maps (default = 'Linkage group')

void

internal function to be documented

Value

a data frame containing a brief summary of all maps

A data.frame object containing the name of the markers and their genetic position

Author(s)

Gabriel Gesteira, gabrielgesteira@usp.br

Cristiane Taniguti, chtaniguti@tamu.edu

Marcelo Mollinari, mmollin@ncsu.edu

Cristiane Taniguti, chtaniguti@tamu.edu

References

Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. doi: 10.1534/g3.119.400378


viewpoly documentation built on Jan. 3, 2022, 5:10 p.m.