viewqtl: Logarithm of _P_-value (LOP) profile plots. Modified version...

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

Description

Plots profiled logarithm of score-based P-values (LOP) from individual or combined traits.

Usage

plot_profile(
  profile,
  qtl_info,
  selected_mks,
  pheno.col = NULL,
  lgs.id = NULL,
  by_range = TRUE,
  range.min = NULL,
  range.max = NULL,
  plot = TRUE,
  software = NULL
)

only_plot_profile(pl.in)

data_effects(
  qtl_info,
  effects,
  pheno.col = NULL,
  p1 = "P1",
  p2 = "P2",
  df.info = NULL,
  lgs = NULL,
  groups = NULL,
  position = NULL,
  software,
  design = c("bar", "circle", "digenic")
)

coord_radar(theta = "x", start = 0, direction = 1)

plot_effects(
  data_effects.obj,
  software,
  design = c("bar", "circle", "digenic")
)

breeding_values(qtl_info, probs, selected_mks, blups, beta.hat, pos)

calc_homologprob(probs, selected_mks, selected_lgs)

## S3 method for class 'mappoly.homoprob'
plot(x, stack = FALSE, lg = NULL, ind = NULL, verbose = TRUE, ...)

select_haplo(input.haplo, probs, selected_mks, effects.data)

Arguments

x	an object of class mappoly.homoprob
stack	logical. If TRUE, probability profiles of all homologues are stacked in the plot (default = FALSE)
lg	indicates which linkage group should be plotted. If NULL (default), it plots the first linkage group. If "all", it plots all linkage groups
ind	indicates which individuals should be plotted. It can be the position of the individuals in the dataset or it's name. If NULL (default), the function plots the first individual
verbose	if TRUE (default), the current progress is shown; if FALSE, no output is produced
...	unused arguments
use.plotly	if TRUE (default), it uses plotly interactive graphic

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