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

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

Description

This function generates a brief summary table

This function plots a genetic linkage map(s)

Usage

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, [e-mail]

Cristiane Taniguti, [e-mail]

Marcelo Mollinari, [e-mail]

Cristiane Taniguti, [e-mail]

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.