#========
# plotting
#========
FIXME:

#=======================
dirs.R
#=======================
#dirs.R: imports dir structure
change this to cmd so you can pass in drug and gene name

#=======================
plotting_data.R
#=======================
??? update how to run


#=======================
combining_dfs_plotting.R
#=======================
??? update how to run


#=======================
mcsm_mean_stability.R
#=======================
??? update how to run
# input: calls the "plotting_data.R"
# output: <gene>_mean_stability.csv

#======================
replaceBfactor_pdb.R
#=======================
# input: 2 files; pdb file and <gene>_mean_stability.csv (output from "mcsm_mean_stability.R")
# output: 2 pdb files with bfactors replaced with 1) mean_duet and 2) mean_affinity values

#=======================
basic_barplots_PS.R
#=======================
# input: calls the "plotting_data.R"
output plots: 2 svgs
    1) basic_barplot_PS.svg
    2) position_count_PS.svg
    
#=======================    
barplot_colour_function.R"
#=======================  
function that generates stability coloures (red to blue) based on the
corresponding value. It is sourced by other scripts.

#=======================
subcols_axis.R
# assigns colours to position numebers with bg and fg colours
# sourced by other scripts.
#=======================
# input: calls the "plotting_data.R"
# sourced by other scripts, no output perse!
   
#=======================
barplots_subcolours_aa_PS.R
# barplot coloured by stability and position numbers coloured by active site colours
#=======================
# input: calls the "subcols_axis.R" and "barplot_colour_function.R"
# output plots: 1 svg
    1) barplot_acoloured_PS.svg

#=======================
barplots_subcolours_PS.R
# same as the above script expcet no positional colouring
#=======================
# input: calls the "plotting_data.R" and "barplot_colour_function.R"
# output plots: 1 svg
    1) barplot_coloured_PS.svg

#=======================
lineage_dist_PS.R
# lineage distribution for all muts and dr muts in one figure
#=======================
# input: calls the "combining_dfs_plotting.R"
# output plots: 1 svg
    1) lineage_dist_combined_PS.svg

    
########################################################################
#                              ligand plots
########################################################################

#=======================
basic_barplots_LIG.R
# generates two basic barplots 
# No. of stabilsing and destabilising mutations for ligand_distance<10A
# No. of SNPs per site
#=======================
# input: calls the "plotting_data.R"
# output plots: 2 svgs
    1) basic_barplot_LIG.svg
    2) position_count_LIg.svg

