plot_svd | R Documentation |
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 )
data_obj |
a |
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 |
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 |
Below the bars is a heatmap indicating how each trait contributes to each eigentrait. Colors can be adjusted to suit preferences.
list("data_obj" = data_obj, "geno_obj" = geno_obj)
## 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)
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