plot_svd: Plots eigentraits
In cape: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

plot_svd

R Documentation

Plots eigentraits

Description

This function plots the results of the singular value decomposition (SVD) on the phenotypes. Gray bars indicate the amount of phenotypic variance accounted for by each eigentrait.

Usage

plot_svd(
  data_obj,
  orientation = c("vertical", "horizontal"),
  neg_col = "blue",
  pos_col = "brown",
  light_dark = "f",
  pheno_labels = NULL,
  cex_barplot_axis = 1.7,
  cex_barplot_labels = 2,
  cex_barplot_title = 1.7,
  main = "Eigentrait Contributions to Phenotypes",
  cex_main = 2,
  main_x = 0.5,
  main_y = 0.5,
  cex_ET = 1.7,
  ET_label_x = 0.5,
  ET_label_y = 0.5,
  pheno_label_pos = 0.5,
  cex_pheno = 1.7,
  pheno_srt = 90,
  percent_total_variance_x = 0.5,
  percent_total_variance_y = 0.5,
  cex_color_scale = 1,
  cex_var_accounted = 2,
  var_accounted_x = 0,
  var_accounted_y = 0,
  show_var_accounted = FALSE,
  just_selected_et = FALSE
)

Arguments

`data_obj`	a `Cape` object
`orientation`	string, ("vertical", "horizontal")
`neg_col`	The color to use for negative main effects and interactions takes the same values as pos_col.
`pos_col`	The color to use for positive main effects and interactions must be one of "green", "purple", "red", "orange", "blue", "brown", "yellow", "gray" see `get_color`
`light_dark`	Indicates whether pos_col, neg_col, and bg_col should be selected from light colors ("l"), dark colors ("d") or the full spectrum from light to dark ("f")
`pheno_labels`	Vector of phenotype names if other than what is stored in the data object
`cex_barplot_axis`	Size of axis for the bar plot
`cex_barplot_labels`	Size of labels for the bar plot
`cex_barplot_title`	Size of the barplot title
`main`	Title for the plot. Defaults to "Eigentrait Contributions to Phenotypes"
`cex_main`	Size of the overall title
`main_x`	x shift for the overall title
`main_y`	y shift for the overall title
`cex_ET`	Size of the eigentrait labels
`ET_label_x`	x shift for the eigentrait labels
`ET_label_y`	y shift for the eigentrait labels
`pheno_label_pos`	x shift for the trait labels
`cex_pheno`	size of the trait labels
`pheno_srt`	Rotation factor for the trait labels
`percent_total_variance_x`	x shift for the percent total variance labels
`percent_total_variance_y`	y shift for the percent total variance labels
`cex_color_scale`	label size for the color scal
`cex_var_accounted`	size for the variance accounted for labels
`var_accounted_x`	x shift for the variance accounted axis label
`var_accounted_y`	x shift for the variance accounted axis label
`show_var_accounted`	logical
`just_selected_et`	logical