setwd("~/git/LSHTM_analysis/scripts/plotting")

source ('get_plotting_dfs.R')
source("../functions/bp_lineage.R")

#########################################
# Lineage and SNP count: lineage lf data
#########################################
#=========================
# Data: All lineages or
# selected few
#=========================
sel_lineages = levels(lin_lf$sel_lineages_f)
sel_lineages
lin_lf_plot = lin_lf[lin_lf$sel_lineages_f%in%sel_lineages,]

# drop unused factor levels
lin_lf_plot$sel_lineages_f = factor(lin_lf_plot$sel_lineages_f)
levels(lin_lf_plot$sel_lineages_f)
#=========================
# Lineage count plot
#=========================
lin_count_bp(lin_lf_plot = lin_lf
             , x_categ = "sel_lineages"
             , y_count = "p_count"
             , bar_fill_categ = "count_categ"
             , display_label_col = "p_count"
             , bar_stat_stype = "identity"
             , x_lab_angle = 90
             , my_xats = 20
             , bar_col_labels = c("Mutations", "Total Samples")
             , bar_col_values = c("grey50", "gray75")
             , y_scale_percent = F # T for diversity
             , y_log10 = F
             , y_label = "Count")

###############################################
# Lineage SNP diversity count: lineage wf data
###############################################
#=========================
# Data: All lineages or
# selected few
#=========================
sel_lineages = levels(lin_wf$sel_lineages_f)
sel_lineages
lin_wf_plot = lin_wf[lin_wf$sel_lineages_f%in%sel_lineages,]

# drop unused factor levels
lin_wf_plot$sel_lineages_f = factor(lin_wf_plot$sel_lineages_f)
levels(lin_wf_plot$sel_lineages_f)
#=========================
# Lineage Diversity plot
#=========================
lin_count_bp(lin_wf_plot = lin_wf
                 , x_categ = "sel_lineages"
                 , y_count = "snp_diversity"
                 , display_label_col = "snp_diversity_f"
                 , bar_stat_stype = "identity"
                 , x_lab_angle = 90
                 , my_xats = 20
                 , y_scale_percent = T
                 , y_label = "SNP diversity")