####---- Spatial Enrichment Distribution Plots ----####

plot_height = 300
plot_width = 750
sig_up_colour = default_3way_sig_one_colour
sig_down_colour = default_3way_sig_two_colour
non_sig_colour = default_3way_non_sig_colour
dot_size = 1.5
dot_transparency = 1
data_label_size = 3.5
show_data_labels = TRUE
sig_up_name = "upregulated"
sig_down_name = "downregulated"
non_sig_name = "non-significant"
x_axis_label = "gene location"
y_axis_label = expression("log"[2]* " fold change")
legend_position = "bottom"
density_curve_transparency = 0.75
density_curve_line_thickness = 0


chromosomes = unique(factor(de_annotated$chromosome))

for (chromosome in chromosomes)
{
show_data_labels = TRUE
ggp = make_spatial_enrichment_fold_distribution_plot(chromosome,sig_up_colour,sig_down_colour,non_sig_colour,dot_size,dot_transparency,sig_up_name,sig_down_name,non_sig_name,x_axis_label,y_axis_label,legend_position,data_label_size, show_data_labels)
save_plot(ggp,plot_height,plot_width,paste("plots/spatial_enrichment/fold_distribution_chr_",chromosome,"_labelled.png",sep=""))

show_data_labels = FALSE
ggp = make_spatial_enrichment_fold_distribution_plot(chromosome,sig_up_colour,sig_down_colour,non_sig_colour,dot_size,dot_transparency,sig_up_name,sig_down_name,non_sig_name,x_axis_label,y_axis_label,legend_position,data_label_size, show_data_labels)
save_plot(ggp,plot_height,plot_width,paste("plots/spatial_enrichment/fold_distribution_chr_",chromosome,"_unlabelled.png",sep=""))
}

x_axis_label = "gene location"
y_axis_label = "gene density"

for (chromosome in chromosomes)
{
ggp = make_spatial_enrichment_gene_distribution_plot(chromosome,sig_up_colour,sig_down_colour,non_sig_colour,density_curve_transparency,density_curve_line_thickness,sig_up_name,sig_down_name,non_sig_name,x_axis_label,y_axis_label,legend_position)
save_plot(ggp,plot_height,plot_width,paste("plots/spatial_enrichment/gene_distribution_chr_",chromosome,".png",sep=""))
}

