#!/usr/bin/env Rscript       
#source("~/git/LSHTM_analysis/config/alr.R")
#source("~/git/LSHTM_analysis/config/embb.R")
source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/rpob.R")

source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#####################################################################
lineage_dfL = lineage_plot_data(df = merged_df2
                                , lineage_column_name = "lineage"
                                , remove_empty_lineage = F
                                , lineage_label_col_name = "lineage_labels"
                                , id_colname = "id"
                                , snp_colname = "mutationinformation"
                                )
lin_wf = lineage_dfL[['lin_wf']]
lin_lf = lineage_dfL[['lin_lf']]