# get plotting_dfs()
# using dfs [lf and wf] from lineage_dfL
# FIXME: add SNP diversity as the title
#===============================
# lineage sample and SNP count
#===============================
lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
             , all_lineages = F
             , x_categ = "sel_lineages"
             , y_count = "p_count"
             , use_lineages = c("L1", "L2", "L3", "L4")
             , bar_fill_categ = "count_categ"
             , display_label_col = "p_count"
             , bar_stat_stype = "identity"
             , d_lab_size = 8
             , d_lab_col = "black"
             , my_xats = 25 # x axis text size
             , my_yats = 25 # y axis text sized_lab_size
             , my_xals = 25 # x axis label size
             , my_yals = 25 # y axis label size
             , my_lls  = 25 # legend label size
             , bar_col_labels =  c("SNPs", "Total Samples")
             , bar_col_values = c("grey50", "gray75")
             , bar_leg_name = ""
             , leg_location = "top"
             , y_log10 = F
             , y_scale_percent = FALSE
             , y_label = c("Count")
             )

#===============================
# lineage SNP diversity count
#===============================
lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
                              , x_categ = "sel_lineages"
                              , y_count = "snp_diversity"
                              #, all_lineages = F
                              , use_lineages = c("L1", "L2", "L3", "L4")
                              , display_label_col = "snp_diversity_f"
                              , bar_stat_stype = "identity"
                              , x_lab_angle = 90
                              , d_lab_size =9
                              , my_xats = 25 # x axis text size
                              , my_yats = 25 # y axis text size
                              , my_xals = 25 # x axis label size
                              , my_yals = 25 # y axis label size
                              , my_lls  = 25 # legend label size
                              , y_log10 = F
                              , y_scale_percent = F
                              , leg_location = "top"
                              , y_label = "Percent" #"SNP diversity"
                              , bp_plot_title = "nsSNP diversity"
                              , title_colour = "black" #"chocolate4"
                              , subtitle_text = NULL
                              , sts = 20
                              , subtitle_colour = "#350E20FF")

#=============================================
# Output plots: Lineage count and Diversity
#=============================================
# lineage_bp_CL =  paste0(outdir_images
#                         ,tolower(gene)
#                         ,"_lineage_bp_CL_Tall.svg")
# 
# cat("Lineage barplots:", lineage_bp_CL)
# svg(lineage_bp_CL, width = 8, height = 15)
# 
# cowplot::plot_grid(lin_countP, lin_diversityP
#                      #, labels = c("(a)", "(b)", "(c)", "(d)")
#                       , nrow = 2
#                      # , ncols = 2
#                       , labels = "AUTO"
#                       , label_size = 25)
# 
# dev.off()