113 lines
3.5 KiB
R
113 lines
3.5 KiB
R
#!/usr/bin/env Rscript
|
|
setwd("~/git/LSHTM_analysis/scripts/functions/")
|
|
getwd()
|
|
#############################################################
|
|
#===========================================
|
|
# load functions, data, dirs, hardocded vars
|
|
# that will be used in testing the functions
|
|
#===========================================
|
|
drug = "streptomycin"
|
|
gene = "gid"
|
|
|
|
source("plotting_data.R")
|
|
|
|
infile = paste0("~/git/Data/", drug, "/output/", gene, "_comb_stab_struc_params.csv")
|
|
infile_df = read.csv(infile)
|
|
|
|
lig_dist = 5
|
|
pd_df = plotting_data(infile_df
|
|
, lig_dist_colname = 'ligand_distance'
|
|
, lig_dist_cutoff = lig_dist)
|
|
|
|
my_df = pd_df[[1]]
|
|
my_df_u = pd_df[[2]]
|
|
my_df_u_lig = pd_df[[3]]
|
|
dup_muts = pd_df[[4]]
|
|
|
|
#=====================
|
|
# functions to test
|
|
#=====================
|
|
source("stability_count_bp.R")
|
|
source("position_count_bp.R")
|
|
|
|
##################################################################
|
|
# ------------------------------
|
|
# barplot for mscm stability
|
|
# ------------------------------
|
|
basic_bp_duet = paste0(tolower(gene), "_basic_barplot_PS.svg")
|
|
plot_basic_bp_duet = paste0(plotdir,"/", basic_bp_duet)
|
|
|
|
svg(plot_basic_bp_duet)
|
|
print(paste0("plot filename:", basic_bp_duet))
|
|
|
|
# function only
|
|
stability_count_bp(plotdf = my_df_u
|
|
, df_colname = "duet_outcome"
|
|
, leg_title = "DUET outcome"
|
|
, label_categories = c("Destabilising", "Stabilising")
|
|
, leg_position = "top")
|
|
|
|
dev.off()
|
|
|
|
# ------------------------------
|
|
# barplot for ligand affinity
|
|
# ------------------------------
|
|
basic_bp_ligand = paste0(tolower(gene), "_basic_barplot_LIG.svg")
|
|
plot_basic_bp_ligand = paste0(plotdir, "/", basic_bp_ligand)
|
|
|
|
svg(plot_basic_bp_ligand)
|
|
print(paste0("plot filename:", basic_bp_ligand))
|
|
|
|
# function only
|
|
lig_dist = 10
|
|
stability_count_bp(plotdf = my_df_u_lig
|
|
, df_colname = "ligand_outcome"
|
|
, leg_title = "Ligand outcome"
|
|
, yaxis_title = paste0("Number of nsSNPs\nLigand dist: <", lig_dist, "\u212b")
|
|
#, bp_plot_title = "Sites < 10 Ang of ligand"
|
|
)
|
|
|
|
dev.off()
|
|
# ------------------------------
|
|
# barplot for foldX
|
|
# ------------------------------
|
|
basic_bp_foldx = paste0(tolower(gene), "_basic_barplot_foldx.svg")
|
|
plot_basic_bp_foldx = paste0(plotdir,"/", basic_bp_foldx)
|
|
|
|
svg(plot_basic_bp_foldx)
|
|
print(paste0("plot filename:", plot_basic_bp_foldx))
|
|
|
|
stability_count_bp(plotdf = my_df_u
|
|
, df_colname = "foldx_outcome"
|
|
, leg_title = "FoldX outcome")
|
|
dev.off()
|
|
#===============================================================
|
|
# ------------------------------
|
|
# barplot for nssnp site count: all
|
|
# ------------------------------
|
|
pos_count_duet = paste0(tolower(gene), "_position_count_PS.svg")
|
|
plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
|
|
|
|
svg(plot_pos_count_duet)
|
|
print(paste0("plot filename:", plot_pos_count_duet))
|
|
|
|
# function only
|
|
site_snp_count_bp(plotdf = my_df_u
|
|
, df_colname = "position")
|
|
|
|
dev.off()
|
|
# ------------------------------
|
|
# barplot for nssnp site count: within 10 Ang
|
|
# ------------------------------
|
|
pos_count_ligand = paste0(tolower(gene), "_position_count_LIG.svg")
|
|
plot_pos_count_ligand = paste0(plotdir, "/", pos_count_ligand)
|
|
|
|
svg(plot_pos_count_ligand)
|
|
print(paste0("plot filename:", plot_pos_count_ligand))
|
|
|
|
# function only
|
|
site_snp_count_bp(plotdf = my_df_u_lig
|
|
, df_colname = "position")
|
|
|
|
dev.off()
|
|
#===============================================================
|