plot_svd: Plots eigentraits

Description Usage Arguments Details Value Examples

View source: R/plot_svd.R

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
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

1
2
3
4
5
6
7
8
## 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)

cape documentation built on Feb. 10, 2021, 5:06 p.m.