####---- MA Plot ----####

plot_height = 500
plot_width = 600
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
sig_up_name = "upregulated"
sig_down_name = "downregulated"
non_sig_name = "non-significant"
topn = 10 # option is an integer or "ALL_SIG"
label_size = 3.5
x_axis_label = expression("mean expression (log"[10]* ")")
y_axis_label = expression("log"[2]* " fold change")
legend_position = "bottom"

ggp = make_MA_plot(de_annotated, 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, topn, label_size)
save_plot(ggp,plot_height,plot_width,"<*path*>plots/MA_plot/MA_plot_labelled.png<*/path*>")

topn = 0
ggp = make_MA_plot(de_annotated, 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, topn, label_size)
save_plot(ggp,plot_height,plot_width,"<*path*>plots/MA_plot/MA_plot_unlabelled.png<*/path*>")

