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generated subcolour bps for PS

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Tanushree Tunstall 2020-08-26 12:45:09 +01:00
parent ed739aeb71
commit 482eeadb9a
3 changed files with 121 additions and 96 deletions
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61
scripts/plotting/running_plot_scripts
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@ -3,20 +3,75 @@
#========
#=======================
#1) plotting_data.R
plotting_data.R
#=======================
??? update how to run
#=======================
# mcsm_mean_stability.R
mcsm_mean_stability.R
#=======================
??? update how to run
# input: calls the "plotting_data.R"
# output: <gene>_mean_stability.csv
#======================
# replaceBfactor_pdb.R
replaceBfactor_pdb.R
#=======================
# input: 2 files; pdb file and <gene>_mean_stability.csv (output from "mcsm_mean_stability.R")
# output: 2 pdb files with bfactors replaced with 1) mean_duet and 2) mean_affinity values
#=======================
basic_barplots_PS.R
#=======================
# input: calls the "plotting_data.R"
output plots: 2 svgs
1) basic_barplot_PS.svg
2) position_count_PS.svg
#=======================
barplot_colour_function.R"
#=======================
function that generates stability coloures (red to blue) based on the
corresponding value. It is sourced by other scripts.
#=======================
subcols_axis_PS.R
# assigns colours to position numebers with bg and fg colours
# sourced by other scripts.
#=======================
# input: calls the "plotting_data.R"
# sourced by other scripts, no output perse!
#=======================
barplots_subcolours_aa_PS.R
# barplot coloured by stability and position numbers coloured by active site colours
#=======================
# input: calls the "subcols_axis.R" and "barplot_colour_function.R"
# output plots: 1 svg
1) barplot_acoloured_PS.svg
#=======================
barplots_subcolours_PS.R
# same as the above script expcet no positional colouring
#=======================
# input: calls the "plotting_data.R" and "barplot_colour_function.R"
# output plots: 1 svg
1) barplot_coloured_PS.svg
########################################################################
# ligand plots
########################################################################
#=======================
basic_barplots_LIG.R
# generates two basic barplots
# No. of stabilsing and destabilising mutations for ligand_distance<10A
# No. of SNPs per site
#=======================
# input: calls the "plotting_data.R"
# output plots: 2 svgs
1) basic_barplot_LIG.svg
2) position_count_LIg.svg