plots with mean along the x axis and standard deviation along the y axis
plotting functions for package vqtl
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)
the cross
the name of the phenotype of interest
the factors by which the units are grouped
plot title
the focal covariates, whose effects will be plotted. Markers or phenotypes.
the nuisance covariates, whose effects will be modeled, then marginalized over. Markers or phenotypes.
plotting names of genotype groups
x axis limits
y axis limits
Should ribbons be drawn connecting the sub-groups of the focal groups?
thickness of the lines indicating standard error
size of the plotted points
The phenotype to plot
The marker to stratify observations by
variable name to color the points by
a discrete phenotype to map to the shape aesthetic of the points
alpha value (see-throughness) of the plotted points
Should I bars be plotted showing the standard deviation of each group?
Should the Ibars be connected horizontally?
plotting labels for genotype groups
Nothing, just plot.
nothing, just the plot.
nothing. Just plots.