#########################################################################
#===================
# basic_barplot.R
#===================
#-----------------------------------------------------------------------
./basic_barplots.R -d streptomycin -g gid
#-----------------------------------------------------------------------

 It replaces
 basic_barplot_PS.R
 basic_barplot_LIG.R
 basic_barplot_foldx.R
 These have been moved to redundant/

sources:
 ## plotting_globals.R (previously dir.R)
 ## plotting_data.R 
 ## position_count_bp.R
 ## stability_count_bp.R
 
 outputs: 5 svgs in the plotdir
 ## gid_basic_barplot_foldx
 ## gid_basic_barplot_LIG
 ## gid_basic_barplot_PS
 ## gid_position_count_PS
 ## gid_position_count_LIG
 
 note: 
 -f flag has default if not supplied 
#########################################################################
#===================
# get_plotting_dfs.R
#===================

NOTE: Not ran directly. But is sourced by other plotting scripts to get 
the df needed to plot graphs. This is run by these ind plottings scripts
like below as cmd where the cmd args return valid dfs used for plots.

#===================
# logo_plots.R
#===================
#-----------------------------------------------------------------------
./logo_plots.R -d streptomycin -g gid
#-----------------------------------------------------------------------

It replaces
 ## logo_plot.R
 ## logo_multiple_muts
 ## logo_combined.R
These have been moved to redundant/

sources:
 ## get_plotting_dfs.R

 outputs: 4 svgs in the plotdir
 ## logo_or_plot.svg
 ## logo_logOR_plot.svg
 ## logo_multiple_muts.svg
 ## logo_combined_labelled.svg
 
 note: 
 - fa flag has default if not supplied 
 - fb flag has default if not supplied 
 - Error in grid.Call fixed by commenting out image rendering on console
 
#===================
# corr_plots.R
#=================== 
#-----------------------------------------------------------------------
./corr_plots.R -d streptomycin -g gid
#-----------------------------------------------------------------------

It replaces
 ## corr_data.R
 ## corr_PS_LIG.R
These have been moved to redundant/

sources:
 ## get_plotting_dfs.R

 outputs: 4 svgs in the plotdir
 ## corr_PS.svg
 ## corr_PS_all.svg
 ## corr_LIG.svg
 ## corr_LIG_all.svg
 
note: 
 - fa flag has default if not supplied 
 - fb flag has default if not supplied 
 - Short df being used in this i.e derivations from _df3
 
#========================
# barplots_subcolours.R
#=========================
#-----------------------------------------------------------------------
./barplots_subcolours.R -d streptomycin -g gid
#-----------------------------------------------------------------------

It replaces
 ## barplots_subcolours_PS.R
These have been moved to redundant/

sources:
 ## get_plotting_dfs.R
 ## functions/barplot_colour_function.R

 outputs: 2 svgs in the plotdir
 ## barplot_coloured_PS.svg
 ## barplot_coloured_LIG.svg
 
note: 
 - fa flag has default if not supplied 
 - fb flag has default if not supplied
 
 
#====================================
# lineage_basic_barplots_combined.R
#====================================
#-----------------------------------------------------------------------
./lineage_basic_barplots_combined.R-d streptomycin -g gid
#-----------------------------------------------------------------------

It replaces (and has an added diversity plot)
 ## lineage_basic_barplot.R
These have been moved to redundant/


sources:
 ## get_plotting_dfs.R
 ## functions//bp_lineage.R"

 outputs: 1 svg in the plotdir
 ## basic_lineage_barplots_combined.svg
 
note: 
 - fa flag has default if not supplied 
 - fb flag has default if not supplied
 
########################################################################
# TODO
Delete: dirs.R
after grepping
barplots_subcolours_aa_combined.R:source("dirs.R")
basic_barplots_PS.R:source("dirs.R")
resolving_ambiguous_muts.R:source("dirs.R")
########################################################################

