added corr_data.R corr_PS_LIG_all.R corr_PS_LIG_v2.R
This commit is contained in:
parent
c58fa8cd4d
commit
81796df71a
3 changed files with 574 additions and 0 deletions
232
scripts/plotting/corr_data.R
Normal file
232
scripts/plotting/corr_data.R
Normal file
|
|
@ -0,0 +1,232 @@
|
|||
#!/usr/bin/env Rscript
|
||||
#########################################################
|
||||
# TASK: Prepare for correlation data
|
||||
|
||||
#=======================================================================
|
||||
# working dir and loading libraries
|
||||
getwd()
|
||||
setwd("~/git/LSHTM_analysis/scripts/plotting/")
|
||||
getwd()
|
||||
|
||||
#source("Header_TT.R")
|
||||
source("combining_dfs_plotting.R")
|
||||
source("my_pairs_panel.R") # with lower panel turned off
|
||||
# should return the following dfs, directories and variables
|
||||
|
||||
# PS combined:
|
||||
# 1) merged_df2
|
||||
# 2) merged_df2_comp
|
||||
# 3) merged_df3
|
||||
# 4) merged_df3_comp
|
||||
|
||||
# LIG combined:
|
||||
# 5) merged_df2_lig
|
||||
# 6) merged_df2_comp_lig
|
||||
# 7) merged_df3_lig
|
||||
# 8) merged_df3_comp_lig
|
||||
|
||||
# 9) my_df_u
|
||||
# 10) my_df_u_lig
|
||||
|
||||
cat(paste0("Directories imported:"
|
||||
, "\ndatadir:", datadir
|
||||
, "\nindir:", indir
|
||||
, "\noutdir:", outdir
|
||||
, "\nplotdir:", plotdir))
|
||||
|
||||
cat(paste0("Variables imported:"
|
||||
, "\ndrug:", drug
|
||||
, "\ngene:", gene
|
||||
, "\ngene_match:", gene_match
|
||||
, "\nAngstrom symbol:", angstroms_symbol
|
||||
, "\nNo. of duplicated muts:", dup_muts_nu
|
||||
, "\nNA count for ORs:", na_count
|
||||
, "\nNA count in df2:", na_count_df2
|
||||
, "\nNA count in df3:", na_count_df3))
|
||||
|
||||
#=======
|
||||
# output
|
||||
#=======
|
||||
# corr_ps_df2
|
||||
# corr_lig_df2
|
||||
|
||||
####################################################################
|
||||
# end of loading libraries and functions
|
||||
####################################################################
|
||||
|
||||
#%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
#df_ps = merged_df3
|
||||
df_ps = merged_df2
|
||||
|
||||
#df_lig = merged_df3_lig
|
||||
df_lig = merged_df2_lig
|
||||
|
||||
#%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
|
||||
########################################################################
|
||||
# end of data extraction and cleaning for plots #
|
||||
########################################################################
|
||||
|
||||
#======================
|
||||
# adding log cols
|
||||
#======================
|
||||
|
||||
df_ps$log10_or_mychisq = log10(df_ps$or_mychisq)
|
||||
df_ps$neglog_pval_fisher = -log10(df_ps$pval_fisher)
|
||||
|
||||
df_ps$log10_or_kin = log10(df_ps$or_kin)
|
||||
df_ps$neglog_pwald_kin = -log10(df_ps$pwald_kin)
|
||||
|
||||
#df_ps$mutation_info_labels = ifelse(df_ps$mutation_info == dr_muts_col, 1, 0)
|
||||
|
||||
#===========================
|
||||
# Data for Correlation plots:PS
|
||||
#===========================
|
||||
# subset data to generate pairwise correlations
|
||||
cols_to_select = c("mutationinformation"
|
||||
, "duet_scaled"
|
||||
, "foldx_scaled"
|
||||
#, "mutation_info_labels"
|
||||
, "asa"
|
||||
, "rsa"
|
||||
, "rd_values"
|
||||
, "kd_values"
|
||||
, "log10_or_mychisq"
|
||||
, "neglog_pval_fisher"
|
||||
, "or_kin"
|
||||
, "neglog_pwald_kin"
|
||||
, "af"
|
||||
, "af_kin"
|
||||
, "duet_outcome"
|
||||
, drug)
|
||||
|
||||
corr_data_ps = df_ps[cols_to_select]
|
||||
|
||||
dim(corr_data_ps)
|
||||
|
||||
# assign nice colnames (for display)
|
||||
my_corr_colnames = c("Mutation"
|
||||
, "DUET"
|
||||
, "Foldx"
|
||||
#, "Mutation class"
|
||||
, "ASA"
|
||||
, "RSA"
|
||||
, "RD"
|
||||
, "KD"
|
||||
, "Log (OR)"
|
||||
, "-Log (P)"
|
||||
, "Adjusted (OR)"
|
||||
, "-Log (P wald)"
|
||||
, "AF"
|
||||
, "AF_kin"
|
||||
, "duet_outcome"
|
||||
, drug)
|
||||
|
||||
length(my_corr_colnames)
|
||||
|
||||
colnames(corr_data_ps)
|
||||
colnames(corr_data_ps) <- my_corr_colnames
|
||||
colnames(corr_data_ps)
|
||||
|
||||
start = 1
|
||||
end = which(colnames(corr_data_ps) == drug); end # should be the last column
|
||||
offset = 1
|
||||
|
||||
#corr_ps_df2 = corr_data_ps[start:(end-offset)] # without drug
|
||||
corr_ps_df2 = corr_data_ps[start:end]
|
||||
head(corr_ps_df2)
|
||||
|
||||
#-----------------
|
||||
# short_df ps: merged_df3
|
||||
#-----------------
|
||||
corr_ps_df3 = corr_ps_df2[!duplicated(corr_ps_df2$Mutation),]
|
||||
|
||||
na_or = sum(is.na(corr_ps_df3$`Log (OR)`))
|
||||
check1 = nrow(corr_ps_df3) - na_or
|
||||
|
||||
na_adj_or = sum(is.na(corr_ps_df3$`adjusted (OR)`))
|
||||
check2 = nrow(corr_ps_df3) - na_adj_or
|
||||
|
||||
#if ( nrow(corr_ps_df3) == nrow(merged_df3) ) {
|
||||
# cat( "PASS: No. of rows for corr_ps_df3 match" )
|
||||
#}if ( nrow(merged_df3_comp) == check1 ){
|
||||
# cat( "PASS: No. of OR values checked" )
|
||||
#}
|
||||
|
||||
################################################################################################
|
||||
#===========================
|
||||
# Data for Correlation plots: LIG
|
||||
#===========================
|
||||
table(df_lig$ligand_outcome)
|
||||
|
||||
df_lig$log10_or_mychisq = log10(df_lig$or_mychisq)
|
||||
df_lig$neglog_pval_fisher = -log10(df_lig$pval_fisher)
|
||||
|
||||
df_lig$log10_or_kin = log10(df_lig$or_kin)
|
||||
df_lig$neglog_pwald_kin = -log10(df_lig$pwald_kin)
|
||||
|
||||
# subset data to generate pairwise correlations
|
||||
cols_to_select = c("mutationinformation"
|
||||
, "affinity_scaled"
|
||||
#, "mutation_info_labels"
|
||||
, "asa"
|
||||
, "rsa"
|
||||
, "rd_values"
|
||||
, "kd_values"
|
||||
, "log10_or_mychisq"
|
||||
, "neglog_pval_fisher"
|
||||
, "or_kin"
|
||||
, "neglog_pwald_kin"
|
||||
, "af"
|
||||
, "af_kin"
|
||||
, "ligand_outcome"
|
||||
, drug)
|
||||
|
||||
corr_data_lig = df_lig[, cols_to_select]
|
||||
|
||||
|
||||
dim(corr_data_lig)
|
||||
|
||||
# assign nice colnames (for display)
|
||||
my_corr_colnames = c("Mutation"
|
||||
, "Ligand Affinity"
|
||||
#, "Mutation class"
|
||||
, "ASA"
|
||||
, "RSA"
|
||||
, "RD"
|
||||
, "KD"
|
||||
, "Log (OR)"
|
||||
, "-Log (P)"
|
||||
, "Adjusted (OR)"
|
||||
, "-Log (P wald)"
|
||||
, "AF"
|
||||
, "AF_kin"
|
||||
, "ligand_outcome"
|
||||
, drug)
|
||||
|
||||
length(my_corr_colnames)
|
||||
|
||||
colnames(corr_data_lig)
|
||||
colnames(corr_data_lig) <- my_corr_colnames
|
||||
colnames(corr_data_lig)
|
||||
|
||||
start = 1
|
||||
end = which(colnames(corr_data_lig) == drug); end # should be the last column
|
||||
offset = 1
|
||||
|
||||
#corr_lig_df2 = corr_data_lig[start:(end-offset)] # without drug
|
||||
corr_lig_df2 = corr_data_lig[start:end]
|
||||
head(corr_lig_df2)
|
||||
|
||||
|
||||
#-----------------
|
||||
# short_df lig: merged_df3_lig
|
||||
#-----------------
|
||||
|
||||
corr_lig_df3 = corr_lig_df2[!duplicated(corr_lig_df2$Mutation),]
|
||||
|
||||
#######################################################
|
||||
rm(merged_df2, merged_df2_lig, merged_df3, merged_df3_lig
|
||||
, merged_df2_comp , merged_df3_comp, merged_df2_comp_lig, merged_df3_comp_lig
|
||||
, corr_data_ps, corr_data_lig)
|
||||
Loading…
Add table
Add a link
Reference in a new issue