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moved all test scripts for functions to tests/

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Tanushree Tunstall 2021-09-09 13:12:07 +01:00
parent 2ee66c770b
commit 03031d2eb6
15 changed files with 162 additions and 776 deletions
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113
scripts/functions/test_bp.R
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@ -1,113 +0,0 @@
#!/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()
#===============================================================