Description Usage Arguments Value
plots with mean along the x axis and standard deviation along the y axis
plotting functions for package vqtl
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
|
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 |
Nothing, just plot.
nothing, just the plot.
nothing. Just plots.
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