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

Description Usage Arguments

Description

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

Usage

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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.