#########################################################################
#===================
# basic_barplot.R
#===================
 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
 
 note: 
 -f flag has default if not supplied 
#-----------------------------------------------------------------------
./basic_barplots.R -d streptomycin -g gid -f /home/tanu/gid_test_file.csv
#-----------------------------------------------------------------------

#===================
# log_plot.R
#===================
./logo_plot.R -d streptomycin -g gid

sources:
 ## plotting_globals.R (previously dir.R)
 ## plotting_data.R 
 ## combining_dfs_plotting.R

 outputs: plotdir
 ## 1 svg of OR for all positions
 
 note: 
 -fa flag has default if not supplied 
 -fb flag has default if not supplied 
 
#========================
# ./logo_multiple_muts.R : FIXME, 
Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : polygon edge not found (new)
https://stackoverflow.com/questions/34220883/error-in-grid-calll-textbounds-as-graphicsannotxlabel-xx-xy-polygon
#========================
./logo_multiple_muts.R -d streptomycin -g gid

sources:
 ## plotting_globals.R (previously dir.R)
 ## plotting_data.R 
 ## combining_dfs_plotting.R

 outputs: plotdir
 ## 1 svg of multiple muts for all positions > 1 muts (mutations + wt)
 
 note: 
 -fa flag has default if not supplied 
 -fb flag has default if not supplied  
 
#========================
# ./logo_combined.R : FIXME, 
Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : polygon edge not found (new)
https://stackoverflow.com/questions/34220883/error-in-grid-calll-textbounds-as-graphicsannotxlabel-xx-xy-polygon
#========================

sources:
 ## plotting_globals.R (previously dir.R)
 ## plotting_data.R 
 ## combining_dfs_plotting.R

 outputs: plotdir
 ## 1 svg combined of OR logo plot + mulitple_muts i.e output from
  'logo_plots.R' + 'logo_multiple_muts.R'
 
 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")
########################################################################