98 lines
2.7 KiB
Text
98 lines
2.7 KiB
Text
#========
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# plotting
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#========
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FIXME:
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#=======================
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dirs.R
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#=======================
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#dirs.R: imports dir structure
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change this to cmd so you can pass in drug and gene name
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#=======================
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plotting_data.R
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#=======================
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??? update how to run
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#=======================
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combining_dfs_plotting.R
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#=======================
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??? update how to run
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#=======================
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mcsm_mean_stability.R
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#=======================
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??? update how to run
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# input: calls the "plotting_data.R"
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# output: <gene>_mean_stability.csv
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#======================
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replaceBfactor_pdb.R
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#=======================
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# input: 2 files; pdb file and <gene>_mean_stability.csv (output from "mcsm_mean_stability.R")
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# output: 2 pdb files with bfactors replaced with 1) mean_duet and 2) mean_affinity values
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#=======================
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basic_barplots_PS.R
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#=======================
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# input: calls the "plotting_data.R"
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output plots: 2 svgs
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1) basic_barplot_PS.svg
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2) position_count_PS.svg
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#=======================
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barplot_colour_function.R"
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#=======================
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function that generates stability coloures (red to blue) based on the
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corresponding value. It is sourced by other scripts.
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#=======================
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subcols_axis.R
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# assigns colours to position numebers with bg and fg colours
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# sourced by other scripts.
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#=======================
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# input: calls the "plotting_data.R"
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# sourced by other scripts, no output perse!
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#=======================
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barplots_subcolours_aa_PS.R
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# barplot coloured by stability and position numbers coloured by active site colours
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#=======================
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# input: calls the "subcols_axis.R" and "barplot_colour_function.R"
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# output plots: 1 svg
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1) barplot_acoloured_PS.svg
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#=======================
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barplots_subcolours_PS.R
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# same as the above script expcet no positional colouring
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#=======================
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# input: calls the "plotting_data.R" and "barplot_colour_function.R"
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# output plots: 1 svg
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1) barplot_coloured_PS.svg
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#=======================
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lineage_dist_PS.R
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# lineage distribution for all muts and dr muts in one figure
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#=======================
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# input: calls the "combining_dfs_plotting.R"
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# output plots: 1 svg
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1) lineage_dist_combined_PS.svg
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########################################################################
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# ligand plots
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########################################################################
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#=======================
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basic_barplots_LIG.R
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# generates two basic barplots
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# No. of stabilsing and destabilising mutations for ligand_distance<10A
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# No. of SNPs per site
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#=======================
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# input: calls the "plotting_data.R"
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# output plots: 2 svgs
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1) basic_barplot_LIG.svg
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2) position_count_LIg.svg
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