moved old logo plots scripts to redundant and updated running_plotting_scripts.txt to reflect these and how to run the single logo_plots.R to generate logo plots

scripts/plotting/running_plotting_scripts.txt

@@ -2,6 +2,10 @@
 #===================
 # basic_barplot.R
 #===================
+#-----------------------------------------------------------------------
+./basic_barplots.R -d streptomycin -g gid
+#-----------------------------------------------------------------------
+
  It replaces
  basic_barplot_PS.R
  basic_barplot_LIG.R
@@ -14,62 +18,50 @@ sources:
  ## position_count_bp.R
  ## stability_count_bp.R
  
- outputs:
- ## 5 svgs in the plotdir
+ 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 
-#-----------------------------------------------------------------------
-./basic_barplots.R -d streptomycin -g gid -f /home/tanu/gid_test_file.csv
-#-----------------------------------------------------------------------
+#########################################################################
+#===================
+# 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.
 
 #===================
-# log_plot.R
+# log_plots.R
 #===================
-./logo_plot.R -d streptomycin -g gid
+#-----------------------------------------------------------------------
+./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: 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 
-#========================
-./logo_multiple_muts.R -d streptomycin -g gid
-
-sources:
- ## get_plotting_dfs.R
-
- outputs: plotdir
- ## 1 svg of multiple muts for all positions > 1 muts (mutations + wt)
+ 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  
+ - fb flag has default if not supplied 
  - Error in grid.Call fixed by commenting out image rendering on console
- 
-#========================
-# ./logo_combined.R
-#========================
-
-sources:
- ## get_plotting_dfs.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  
- - Error in grid.Call fixed by commenting out image rendering on console
- 
 ########################################################################
 # TODO
 Delete: dirs.R