plotting: mean_var_plot_model_free

Description Usage Arguments Value

Description

plots with mean along the x axis and standard deviation along the y axis

plotting functions for package vqtl

Usage

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mean_var_plot_model_free(cross, phenotype.name, grouping.factor.names,
  title = paste(phenotype.name, "by", paste(grouping.factor.names,
  collapse = ", ")))

mean_var_plot_model_based(cross, phenotype.name, focal.groups = NULL,
  nuisance.groups = NULL, genotype.names = c("AA", "AB", "BB"),
  xlim = NULL, ylim = NULL, title = paste(phenotype.name, "by",
  paste(focal.groups, collapse = ", ")), draw_ribbons = TRUE,
  se_line_size = 1, point_size = 1)

phenotype_at_marker_plot(cross, phenotype_name, marker_name,
  color_by = NULL, shape_by = NULL, point_alpha = 1,
  point_size = 1, Ibars = TRUE, connectIbars = TRUE,
  genotype_labels = NULL)

Arguments

cross

the cross

phenotype.name

the name of the phenotype of interest

grouping.factor.names

the factors by which the units are grouped

title

plot title

focal.groups

the focal covariates, whose effects will be plotted. Markers or phenotypes.

nuisance.groups

the nuisance covariates, whose effects will be modeled, then marginalized over. Markers or phenotypes.

genotype.names

plotting names of genotype groups

xlim

x axis limits

ylim

y axis limits

draw_ribbons

Should ribbons be drawn connecting the sub-groups of the focal groups?

se_line_size

thickness of the lines indicating standard error

point_size

size of the plotted points

phenotype_name

The phenotype to plot

marker_name

The marker to stratify observations by

color_by

variable name to color the points by

shape_by

a discrete phenotype to map to the shape aesthetic of the points

point_alpha

alpha value (see-throughness) of the plotted points

Ibars

Should I bars be plotted showing the standard deviation of each group?

connectIbars

Should the Ibars be connected horizontally?

genotype_labels

plotting labels for genotype groups

Value

Nothing, just plot.

nothing, just the plot.

nothing. Just plots.


rcorty/vqtl documentation built on May 27, 2019, 3:04 a.m.