100 lines
2.7 KiB
Text
100 lines
2.7 KiB
Text
#########################################################################
|
|
#===================
|
|
# 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
|
|
|
|
########################################################################
|
|
# 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")
|
|
########################################################################
|
|
|