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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.
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
)
list("data_obj" = data_obj, "geno_obj" = geno_obj)
a Cape
object
string, ("vertical", "horizontal")
The color to use for negative main effects and interactions takes the same values as 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
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")
Vector of phenotype names if other than what is stored in the data object
Size of axis for the bar plot
Size of labels for the bar plot
Size of the barplot title
Title for the plot. Defaults to "Eigentrait Contributions to Phenotypes"
Size of the overall title
x shift for the overall title
y shift for the overall title
Size of the eigentrait labels
x shift for the eigentrait labels
y shift for the eigentrait labels
x shift for the trait labels
size of the trait labels
Rotation factor for the trait labels
x shift for the percent total variance labels
y shift for the percent total variance labels
label size for the color scal
size for the variance accounted for labels
x shift for the variance accounted axis label
x shift for the variance accounted axis label
logical
logical
Below the bars is a heatmap indicating how each trait contributes to each eigentrait. Colors can be adjusted to suit preferences.