####---- PCA (Scatter Plots) ----####

plot_height = 300
plot_width = 300
plot_sample_group_colours = default_sample_group_colours
plot_sample_group_labels = default_sample_group_labels
plot_sample_labels = default_sample_labels
plot_sample_groupings = sample_groupings
dot_size = 4
dot_transparency = 1
legend_position = "bottom"
sample_label_size = 3.5
show_proportion_of_variance = TRUE
show_sample_labels = TRUE

component_x = 1
component_y = 2
x_axis_label = "PC1"
y_axis_label = "PC2"
ggp = make_PCA_scatterplot(plot_sample_groupings,component_x,component_y,x_axis_label,y_axis_label,plot_sample_group_colours,plot_sample_group_labels,plot_sample_labels,dot_size,dot_transparency,legend_position,sample_label_size,show_proportion_of_variance, show_sample_labels)
save_plot(ggp,plot_height,plot_width,"<*path*>plots/PCA/PCA_1_vs_PCA_2_scatter_plot_labelled.png<*/path*>")

show_sample_labels = FALSE
ggp = make_PCA_scatterplot(plot_sample_groupings,component_x,component_y,x_axis_label,y_axis_label,plot_sample_group_colours,plot_sample_group_labels,plot_sample_labels,dot_size,dot_transparency,legend_position,sample_label_size,show_proportion_of_variance, show_sample_labels)
save_plot(ggp,plot_height,plot_width,"<*path*>plots/PCA/PCA_1_vs_PCA_2_scatter_plot_unlabelled.png<*/path*>")

component_x = 3
component_y = 4
x_axis_label = "PC3"
y_axis_label = "PC4"
show_sample_labels = TRUE
ggp = make_PCA_scatterplot(plot_sample_groupings,component_x,component_y,x_axis_label,y_axis_label,plot_sample_group_colours,plot_sample_group_labels,plot_sample_labels,dot_size,dot_transparency,legend_position,sample_label_size,show_proportion_of_variance, show_sample_labels)
save_plot(ggp,plot_height,plot_width,"<*path*>plots/PCA/PCA_3_vs_PCA_4_scatter_plot_labelled.png<*/path*>")

show_sample_labels = FALSE
ggp = make_PCA_scatterplot(plot_sample_groupings,component_x,component_y,x_axis_label,y_axis_label,plot_sample_group_colours,plot_sample_group_labels,plot_sample_labels,dot_size,dot_transparency,legend_position,sample_label_size,show_proportion_of_variance, show_sample_labels)
save_plot(ggp,plot_height,plot_width,"<*path*>plots/PCA/PCA_3_vs_PCA_4_scatter_plot_unlabelled.png<*/path*>")

