# gid ONLY
source("~/git/LSHTM_analysis/config/gid.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R")

outdir_images="/home/sethp/git/Writing/thesis/tex/images-corrected/gid/"

w=4.5
h=4.5

consurfP = stability_count_bp(plotdf = df3
                              , df_colname = "consurf_outcome"
                              , yaxis_title = "Number of SAVs"
                              , leg_position = "none"
                              #, subtitle_text = "ConSurf"
                              , bar_fill_values = consurf_colours
                              , subtitle_colour= "black"
                              , sts = sts
                              , lts = lts
                              , ats = ats
                              , als = als
                              , ltis = ltis
                              , geom_ls = geom_ls)

consurf_legend = get_legend(
  ggplot(df3, aes(factor(consurf_outcome))) +
    geom_tile(aes(
      fill = consurf_outcome, y=0
    )
    )+
    
    scale_fill_manual(
      values=consurf_colours,
      labels=c("0\nND","1\nVar","2","3","4","5\nAvg","6","7","8","9\nCons"),
      guide=guide_legend(title="Consurf",
                         title.position = "top",
                         title.hjust = 0.5,
                         label.position = "bottom",
                         nrow = 1
      )
    )
)

consurf_out=cowplot::plot_grid(consurf_legend, consurfP,ncol=1,rel_heights = c(2.5,12))

conCLP =  paste0(outdir_images
                 ,tolower(gene)
                 ,"_consurf_BP.jpg")

print(paste0("plot filename:", conCLP))
jpeg(conCLP, units = "in", width = w, height = h, res = 300 )
consurf_out

dev.off()