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added script to test af_or_calcs

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Tanushree Tunstall 2021-06-11 13:33:25 +01:00
parent 931f8ec2f9
commit 7686aa39b4
3 changed files with 55 additions and 0 deletions
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103
scripts/functions/test_functions.R
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@ -1,103 +0,0 @@
setwd("~/git/LSHTM_analysis/scripts/plotting/functions")
getwd()
#############################################################
#===========================================
# load functions, data, dirs, hardocded vars
# that will be used in testing the functions
#===========================================
source("../plotting_data.R")
infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
pd_df = plotting_data(infile)
my_df = pd_df[[1]]
my_df_u = pd_df[[2]]
my_df_u_lig = pd_df[[3]]
dup_muts = pd_df[[4]]
source("../plotting_globals.R")
drug = "streptomycin"
gene = "gid"
import_dirs(drug, gene)
#=====================
# 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")
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
stability_count_bp(plotdf = my_df_u_lig
, df_colname = "ligand_outcome"
, leg_title = "Ligand outcome"
, 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()
#===============================================================