plot_svd {cape}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

Details

Below the bars is a heatmap indicating how each trait contributes to each eigentrait. Colors can be adjusted to suit preferences.

Value

list("data_obj" = data_obj, "geno_obj" = geno_obj)

Examples

## Not run: 
#plot all eigentraits
plot_svd(data_obj)

#plot only eigentraits being run in cape
plot_svd(data_obj, just_selected_et = TRUE)

## End(Not run)


[Package cape version 3.1.0 Index]