147 lines
3.9 KiB
Text
147 lines
3.9 KiB
Text
#########################################################################
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#===================
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# basic_barplot.R
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#===================
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#-----------------------------------------------------------------------
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./basic_barplots.R -d streptomycin -g gid
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#-----------------------------------------------------------------------
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It replaces
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basic_barplot_PS.R
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basic_barplot_LIG.R
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basic_barplot_foldx.R
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These have been moved to redundant/
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sources:
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## plotting_globals.R (previously dir.R)
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## plotting_data.R
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## position_count_bp.R
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## stability_count_bp.R
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outputs: 5 svgs in the plotdir
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## gid_basic_barplot_foldx
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## gid_basic_barplot_LIG
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## gid_basic_barplot_PS
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## gid_position_count_PS
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## gid_position_count_LIG
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note:
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-f flag has default if not supplied
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#########################################################################
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#===================
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# get_plotting_dfs.R
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#===================
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NOTE: Not ran directly. But is sourced by other plotting scripts to get
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the df needed to plot graphs. This is run by these ind plottings scripts
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like below as cmd where the cmd args return valid dfs used for plots.
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#===================
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# logo_plots.R
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#===================
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#-----------------------------------------------------------------------
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./logo_plots.R -d streptomycin -g gid
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#-----------------------------------------------------------------------
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It replaces
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## logo_plot.R
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## logo_multiple_muts
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## logo_combined.R
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These have been moved to redundant/
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sources:
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## get_plotting_dfs.R
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outputs: 4 svgs in the plotdir
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## logo_or_plot.svg
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## logo_logOR_plot.svg
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## logo_multiple_muts.svg
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## logo_combined_labelled.svg
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note:
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- fa flag has default if not supplied
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- fb flag has default if not supplied
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- Error in grid.Call fixed by commenting out image rendering on console
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#===================
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# corr_plots.R
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#===================
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#-----------------------------------------------------------------------
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./corr_plots.R -d streptomycin -g gid
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#-----------------------------------------------------------------------
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It replaces
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## corr_data.R
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## corr_PS_LIG.R
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These have been moved to redundant/
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sources:
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## get_plotting_dfs.R
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outputs: 4 svgs in the plotdir
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## corr_PS.svg
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## corr_PS_all.svg
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## corr_LIG.svg
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## corr_LIG_all.svg
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note:
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- fa flag has default if not supplied
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- fb flag has default if not supplied
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- Short df being used in this i.e derivations from _df3
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#========================
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# barplots_subcolours.R
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#=========================
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#-----------------------------------------------------------------------
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./barplots_subcolours.R -d streptomycin -g gid
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#-----------------------------------------------------------------------
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It replaces
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## barplots_subcolours_PS.R
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These have been moved to redundant/
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sources:
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## get_plotting_dfs.R
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## functions/barplot_colour_function.R
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outputs: 2 svgs in the plotdir
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## barplot_coloured_PS.svg
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## barplot_coloured_LIG.svg
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note:
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- fa flag has default if not supplied
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- fb flag has default if not supplied
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#====================================
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# lineage_basic_barplots_combined.R
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#====================================
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#-----------------------------------------------------------------------
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./lineage_basic_barplots_combined.R-d streptomycin -g gid
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#-----------------------------------------------------------------------
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It replaces (and has an added diversity plot)
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## lineage_basic_barplot.R
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These have been moved to redundant/
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sources:
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## get_plotting_dfs.R
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## functions//bp_lineage.R"
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outputs: 1 svg in the plotdir
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## basic_lineage_barplots_combined.svg
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note:
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- fa flag has default if not supplied
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- fb flag has default if not supplied
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########################################################################
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# TODO
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Delete: dirs.R
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after grepping
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barplots_subcolours_aa_combined.R:source("dirs.R")
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basic_barplots_PS.R:source("dirs.R")
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resolving_ambiguous_muts.R:source("dirs.R")
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########################################################################
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