###############################
# TASK: function to plot lineage
# dist plots with or without facet
# think about color palette
# for stability
##############################

#n_colours = length(unique(lin_dist_plot$duet_scaled))
#my_palette <- colorRampPalette(c(mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2))(n = n_colours+1)


lineage_distP <- function(plotdf
                          , x_axis = "duet_scaled"
                          , y_axis = "lineage_labels"
                          , x_lab = "DUET"
                          , all_lineages = F
                          , use_lineages = c("L1", "L2", "L3", "L4")
                          , with_facet = F
                          , facet_wrap_var = "" # FIXME: document what this is for
                          , fill_categ = "mutation_info_labels"
                          , fill_categ_cols = c("#E69F00", "#999999")
                          , my_ats = 15 # axis text size
                          , my_als = 20 # axis label size
                          , my_leg_ts = 16
                          , my_leg_title = 16
                          , my_strip_ts = 20
                          , leg_pos = c(0.8, 0.9)
                          , leg_pos_wf = c("top", "left", "bottom", "right")
                          , leg_dir_wf = c("horizontal", "vertical")
                          , leg_label = "")

{
  
  if(!all_lineages){
    plotdf = plotdf[plotdf[[y_axis]]%in%use_lineages,]
  }
  
  ggplot(plotdf, aes_string(x = x_axis
                            , y = y_axis))+
    
    geom_density_ridges(aes_string(fill = fill_categ)
                        , scale = 3
                        , size = 0.3
                        , alpha = 0.8) +
    scale_x_continuous(expand = c(0.01, 0.01)) +
    #coord_cartesian( xlim = c(-1, 1)) +
    scale_fill_manual(values = fill_categ_cols) +
    theme(axis.text.x = element_text(size = my_ats
                                     , angle = 90
                                     , hjust = 1
                                     , vjust = 0.4)
          , axis.text.y = element_text(size = my_ats)
          , axis.title.x = element_text(size = my_ats)
          , axis.title.y = element_blank()
          , strip.text = element_text(size = my_strip_ts)
          , legend.text = element_text(size = my_leg_ts)
          , legend.title = element_text(size = my_leg_title)
          , legend.position = c(0.8, 0.9)) +
    labs(x = x_lab
         , fill = leg_label) + 
  
  # FIXME: This didn't work BEFORE i fixed the ggplot() assignment thing!!!
  if (with_facet){
    
    # used reformulate or make as formula
    #fwv = reformulate(facet_wrap_var)
    fwv = as.formula(paste0("~", facet_wrap_var))
    
    facet_wrap(fwv) + 
      theme(legend.position = leg_pos_wf
            , legend.direction = leg_dir_wf)
  }
}