added files that were moved to redundant
This commit is contained in:
parent
04a7cf15dc
commit
ac383165ec
2 changed files with 877 additions and 0 deletions
442
scripts/plotting/redundant/combining_two_df_FIXME.R
Normal file
442
scripts/plotting/redundant/combining_two_df_FIXME.R
Normal file
|
|
@ -0,0 +1,442 @@
|
|||
getwd()
|
||||
setwd("~/git/LSHTM_analysis/scripts/plotting/")
|
||||
getwd()
|
||||
|
||||
#########################################################
|
||||
# TASK: To combine struct params and meta data for plotting
|
||||
# Input csv files:
|
||||
# 1) <gene>_all_params.csv
|
||||
# 2) <gene>_meta_data.csv
|
||||
|
||||
# Output:
|
||||
# 1) muts with opposite effects on stability
|
||||
# 2) large combined df including NAs for AF, OR,etc
|
||||
# Dim: same no. of rows as gene associated meta_data_with_AFandOR
|
||||
# 3) small combined df including NAs for AF, OR, etc.
|
||||
# Dim: same as mcsm data
|
||||
# 4) large combined df excluding NAs
|
||||
# Dim: dim(#1) - no. of NAs(AF|OR) + 1
|
||||
# 5) small combined df excluding NAs
|
||||
# Dim: dim(#2) - no. of unique NAs - 1
|
||||
# This script is sourced from other .R scripts for plotting
|
||||
#########################################################
|
||||
|
||||
##########################################################
|
||||
# Installing and loading required packages
|
||||
##########################################################
|
||||
source("Header_TT.R")
|
||||
#require(data.table)
|
||||
#require(arsenal)
|
||||
#require(compare)
|
||||
#library(tidyverse)
|
||||
|
||||
|
||||
#%% variable assignment: input and output paths & filenames
|
||||
drug = "pyrazinamide"
|
||||
gene = "pncA"
|
||||
gene_match = paste0(gene,"_p.")
|
||||
cat(gene_match)
|
||||
|
||||
#=============
|
||||
# directories
|
||||
#=============
|
||||
datadir = paste0("~/git/Data")
|
||||
indir = paste0(datadir, "/", drug, "/input")
|
||||
outdir = paste0("~/git/Data", "/", drug, "/output")
|
||||
|
||||
#===========
|
||||
# input
|
||||
#===========
|
||||
#in_filename = "mcsm_complex1_normalised.csv"
|
||||
in_filename_params = paste0(tolower(gene), "_all_params.csv")
|
||||
infile_params = paste0(outdir, "/", in_filename_params)
|
||||
cat(paste0("Input file 1:", infile_params) )
|
||||
|
||||
# infile 2: gene associated meta data
|
||||
#in_filename_gene_metadata = paste0(tolower(gene), "_meta_data_with_AFandOR.csv")
|
||||
in_filename_gene_metadata = paste0(tolower(gene), "_metadata.csv")
|
||||
infile_gene_metadata = paste0(outdir, "/", in_filename_gene_metadata)
|
||||
cat(paste0("Input infile 2:", infile_gene_metadata))
|
||||
|
||||
#===========
|
||||
# output
|
||||
#===========
|
||||
# mutations with opposite effects
|
||||
out_filename_opp_muts = paste0(tolower(gene), "_muts_opp_effects.csv")
|
||||
outfile_opp_muts = paste0(outdir, "/", out_filename_opp_muts)
|
||||
|
||||
|
||||
#%%===============================================================
|
||||
###########################
|
||||
# Read file: struct params
|
||||
###########################
|
||||
cat("Reading struct params including mcsm:"
|
||||
, in_filename_params)
|
||||
|
||||
mcsm_data = read.csv(infile_params
|
||||
#, row.names = 1
|
||||
, stringsAsFactors = F
|
||||
, header = T)
|
||||
|
||||
cat("Input dimensions:", dim(mcsm_data)) #416, 86
|
||||
|
||||
# clear variables
|
||||
rm(in_filename_params, infile_params)
|
||||
|
||||
str(mcsm_data)
|
||||
|
||||
table(mcsm_data$duet_outcome); sum(table(mcsm_data$duet_outcome) )
|
||||
|
||||
# spelling Correction 1: DUET incase American spelling needed!
|
||||
#mcsm_data$duet_outcome[mcsm_data$duet_outcome=="Stabilising"] <- "Stabilizing"
|
||||
#mcsm_data$duet_outcome[mcsm_data$duet_outcome=="Destabilising"] <- "Destabilizing"
|
||||
|
||||
# checks: should be the same as above
|
||||
table(mcsm_data$duet_outcome); sum(table(mcsm_data$duet_outcome) )
|
||||
head(mcsm_data$duet_outcome); tail(mcsm_data$duet_outcome)
|
||||
|
||||
# spelling Correction 2: Ligand incase American spelling needed!
|
||||
table(mcsm_data$ligand_outcome); sum(table(mcsm_data$ligand_outcome) )
|
||||
#mcsm_data$ligand_outcome[mcsm_data$ligand_outcome=="Stabilising"] <- "Stabilizing"
|
||||
#mcsm_data$ligand_outcome[mcsm_data$ligand_outcome=="Destabilising"] <- "Destabilizing"
|
||||
|
||||
# checks: should be the same as above
|
||||
table(mcsm_data$ligand_outcome); sum(table(mcsm_data$ligand_outcome) )
|
||||
head(mcsm_data$ligand_outcome); tail(mcsm_data$ligand_outcome)
|
||||
|
||||
# muts with opposing effects on protomer and ligand stability
|
||||
table(mcsm_data$duet_outcome != mcsm_data$ligand_outcome)
|
||||
changes = mcsm_data[which(mcsm_data$duet_outcome != mcsm_data$ligand_outcome),]
|
||||
|
||||
# sanity check: redundant, but uber cautious!
|
||||
dl_i = which(mcsm_data$duet_outcome != mcsm_data$ligand_outcome)
|
||||
ld_i = which(mcsm_data$ligand_outcome != mcsm_data$duet_outcome)
|
||||
|
||||
cat("Identifying muts with opposite stability effects")
|
||||
if(nrow(changes) == (table(mcsm_data$duet_outcome != mcsm_data$ligand_outcome)[[2]]) & identical(dl_i,ld_i)) {
|
||||
cat("PASS: muts with opposite effects on stability and affinity correctly identified"
|
||||
, "\nNo. of such muts: ", nrow(changes))
|
||||
}else {
|
||||
cat("FAIL: unsuccessful in extracting muts with changed stability effects")
|
||||
}
|
||||
|
||||
#***************************
|
||||
# write file: changed muts
|
||||
write.csv(changes, outfile_opp_muts)
|
||||
|
||||
cat("Finished writing file for muts with opp effects:"
|
||||
, "\nFilename: ", outfile_opp_muts
|
||||
, "\nDim:", dim(changes))
|
||||
|
||||
# clear variables
|
||||
rm(out_filename_opp_muts, outfile_opp_muts)
|
||||
rm(changes, dl_i, ld_i)
|
||||
|
||||
#***************************
|
||||
# count na in each column
|
||||
na_count = sapply(mcsm_data, function(y) sum(length(which(is.na(y))))); na_count
|
||||
|
||||
# sort by mutationinformation
|
||||
##mcsm_data = mcsm_data[order(mcsm_data$mutationinformation),]
|
||||
##head(mcsm_data$mutationinformation)
|
||||
|
||||
df_ncols = ncol(mcsm_data)
|
||||
|
||||
# REMOVE as this is dangerous due to dup muts
|
||||
# get freq count of positions and add to the df
|
||||
#setDT(mcsm_data)[, occurrence := .N, by = .(position)]
|
||||
|
||||
#cat("Added 1 col: position frequency to see which posn has how many muts"
|
||||
# , "\nNo. of cols now", ncol(mcsm_data)
|
||||
# , "\nNo. of cols before: ", df_ncols)
|
||||
|
||||
#pos_count_check = data.frame(mcsm_data$position, mcsm_data$occurrence)
|
||||
|
||||
# check duplicate muts
|
||||
if (length(unique(mcsm_data$mutationinformation)) == length(mcsm_data$mutationinformation)){
|
||||
cat("No duplicate mutations in mcsm data")
|
||||
}else{
|
||||
dup_muts = mcsm_data[duplicated(mcsm_data$mutationinformation),]
|
||||
dup_muts_nu = length(unique(dup_muts$mutationinformation))
|
||||
cat(paste0("CAUTION:", nrow(dup_muts), " Duplicate mutations identified"
|
||||
, "\nOf these, no. of unique mutations are:", dup_muts_nu
|
||||
, "\nExtracting df with unique mutations only"))
|
||||
mcsm_data_u = mcsm_data[!duplicated(mcsm_data$mutationinformation),]
|
||||
}
|
||||
|
||||
if (nrow(mcsm_data_u) == length(unique(mcsm_data$mutationinformation))){
|
||||
cat("Df without duplicate mutations successfully extracted")
|
||||
} else{
|
||||
cat("FAIL: could not extract clean df!")
|
||||
quit()
|
||||
}
|
||||
|
||||
###########################
|
||||
# 2: Read file: <gene>_meta data.csv
|
||||
###########################
|
||||
cat("Reading meta data file:", infile_gene_metadata)
|
||||
|
||||
gene_metadata <- read.csv(infile_gene_metadata
|
||||
, stringsAsFactors = F
|
||||
, header = T)
|
||||
cat("Dim:", dim(gene_metadata))
|
||||
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
# FIXME: remove
|
||||
# counting NAs in AF, OR cols:
|
||||
if (identical(sum(is.na(gene_metadata$OR))
|
||||
, sum(is.na(gene_metadata$pvalue))
|
||||
, sum(is.na(gene_metadata$AF)))){
|
||||
cat("PASS: NA count match for OR, pvalue and AF\n")
|
||||
na_count = sum(is.na(gene_metadata$AF))
|
||||
cat("No. of NAs: ", sum(is.na(gene_metadata$OR)))
|
||||
} else{
|
||||
cat("FAIL: NA count mismatch"
|
||||
, "\nNA in OR: ", sum(is.na(gene_metadata$OR))
|
||||
, "\nNA in pvalue: ", sum(is.na(gene_metadata$pvalue))
|
||||
, "\nNA in AF:", sum(is.na(gene_metadata$AF)))
|
||||
}
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
# clear variables
|
||||
rm(in_filename_gene_metadata, infile_gene_metadata)
|
||||
|
||||
str(gene_metadata)
|
||||
|
||||
# sort by position (same as mcsm_data)
|
||||
# earlier it was mutationinformation
|
||||
#head(gene_metadata$mutationinformation)
|
||||
#gene_metadata = gene_metadata[order(gene_metadata$mutationinformation),]
|
||||
##head(gene_metadata$mutationinformation)
|
||||
|
||||
head(gene_metadata$position)
|
||||
gene_metadata = gene_metadata[order(gene_metadata$position),]
|
||||
head(gene_metadata$position)
|
||||
|
||||
###########################
|
||||
# Merge 1: two dfs with NA
|
||||
# merged_df2
|
||||
###########################
|
||||
head(mcsm_data$mutationinformation)
|
||||
head(gene_metadata$mutationinformation)
|
||||
|
||||
# Find common columns b/w two df
|
||||
merging_cols = intersect(colnames(mcsm_data), colnames(gene_metadata))
|
||||
|
||||
cat(paste0("Merging dfs with NAs: big df (1-many relationship b/w id & mut)"
|
||||
, "\nNo. of merging cols:", length(merging_cols)
|
||||
, "\nMerging columns identified:"))
|
||||
print(merging_cols)
|
||||
|
||||
#=============
|
||||
# merged_df2): gene_metadata + mcsm_data
|
||||
#==============
|
||||
merged_df2 = merge(x = gene_metadata
|
||||
, y = mcsm_data
|
||||
, by = merging_cols
|
||||
, all.y = T)
|
||||
|
||||
cat("Dim of merged_df2: ", dim(merged_df2) #4520, 11
|
||||
)
|
||||
head(merged_df2$position)
|
||||
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
# FIXME: count how many unique muts have entries in meta data
|
||||
# sanity check
|
||||
cat("Checking nrows in merged_df2")
|
||||
if(nrow(gene_metadata) == nrow(merged_df2)){
|
||||
cat("nrow(merged_df2) = nrow (gene associated gene_metadata)"
|
||||
,"\nExpected no. of rows: ",nrow(gene_metadata)
|
||||
,"\nGot no. of rows: ", nrow(merged_df2))
|
||||
} else{
|
||||
cat("nrow(merged_df2)!= nrow(gene associated gene_metadata)"
|
||||
, "\nExpected no. of rows after merge: ", nrow(gene_metadata)
|
||||
, "\nGot no. of rows: ", nrow(merged_df2)
|
||||
, "\nFinding discrepancy")
|
||||
merged_muts_u = unique(merged_df2$mutationinformation)
|
||||
meta_muts_u = unique(gene_metadata$mutationinformation)
|
||||
# find the index where it differs
|
||||
unique(meta_muts_u[! meta_muts_u %in% merged_muts_u])
|
||||
}
|
||||
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
|
||||
# sort by position
|
||||
head(merged_df2$position)
|
||||
merged_df2 = merged_df2[order(merged_df2$position),]
|
||||
head(merged_df2$position)
|
||||
|
||||
merged_df2v3 = merge(x = gene_metadata
|
||||
, y = mcsm_data
|
||||
, by = merging_cols
|
||||
, all = T)
|
||||
|
||||
merged_df2v2 = merge(x = gene_metadata
|
||||
, y = mcsm_data
|
||||
, by = merging_cols
|
||||
, all.x = T)
|
||||
#!=!=!=!=!=!=!=!
|
||||
# COMMENT: used all.y since position 186 is not part of the struc,
|
||||
# hence doesn"t have a mcsm value
|
||||
# but 186 is associated with mutation
|
||||
#!=!=!=!=!=!=!=!
|
||||
|
||||
# should be False
|
||||
identical(merged_df2, merged_df2v2)
|
||||
table(merged_df2$position%in%merged_df2v2$position)
|
||||
|
||||
rm(merged_df2v2)
|
||||
|
||||
#!!!!!!!!!!! check why these differ
|
||||
|
||||
#########
|
||||
# merge 3b (merged_df3):remove duplicate mutation information
|
||||
#########
|
||||
cat("Merging dfs without NAs: small df (removing muts with no AF|OR associated)"
|
||||
,"\nCannot trust lineage info from this"
|
||||
,"\nlinking col: Mutationinforamtion"
|
||||
,"\nfilename: merged_df3")
|
||||
|
||||
#==#=#=#=#=#=#
|
||||
# Cannot trust lineage, country from this df as the same mutation
|
||||
# can have many different lineages
|
||||
# but this should be good for the numerical corr plots
|
||||
#=#=#=#=#=#=#=
|
||||
merged_df3 = merged_df2[!duplicated(merged_df2$mutationinformation),]
|
||||
head(merged_df3$position); tail(merged_df3$position) # should be sorted
|
||||
|
||||
# sanity check
|
||||
cat("Checking nrows in merged_df3")
|
||||
if(nrow(mcsm_data) == nrow(merged_df3)){
|
||||
cat("PASS: No. of rows match with mcsm_data"
|
||||
,"\nExpected no. of rows: ", nrow(mcsm_data)
|
||||
,"\nGot no. of rows: ", nrow(merged_df3))
|
||||
} else {
|
||||
cat("FAIL: No. of rows mismatch"
|
||||
, "\nNo. of rows mcsm_data: ", nrow(mcsm_data)
|
||||
, "\nNo. of rows merged_df3: ", nrow(merged_df3))
|
||||
}
|
||||
|
||||
# counting NAs in AF, OR cols in merged_df3
|
||||
# this is becuase mcsm has no AF, OR cols,
|
||||
# so you cannot count NAs
|
||||
if (identical(sum(is.na(merged_df3$OR))
|
||||
, sum(is.na(merged_df3$pvalue))
|
||||
, sum(is.na(merged_df3$AF)))){
|
||||
cat("PASS: NA count match for OR, pvalue and AF\n")
|
||||
na_count_df3 = sum(is.na(merged_df3$AF))
|
||||
cat("No. of NAs: ", sum(is.na(merged_df3$OR)))
|
||||
} else{
|
||||
cat("FAIL: NA count mismatch"
|
||||
, "\nNA in OR: ", sum(is.na(merged_df3$OR))
|
||||
, "\nNA in pvalue: ", sum(is.na(merged_df3$pvalue))
|
||||
, "\nNA in AF:", sum(is.na(merged_df3$AF)))
|
||||
}
|
||||
|
||||
###########################
|
||||
# 4: merging two dfs: without NA
|
||||
###########################
|
||||
#########
|
||||
# merge 4a (merged_df2_comp): same as merge 1 but excluding NA
|
||||
#########
|
||||
cat("Merging dfs without any NAs: big df (1-many relationship b/w id & mut)"
|
||||
,"\nlinking col: Mutationinforamtion"
|
||||
,"\nfilename: merged_df2_comp")
|
||||
|
||||
merged_df2_comp = merged_df2[!is.na(merged_df2$AF),]
|
||||
#merged_df2_comp = merged_df2[!duplicated(merged_df2$mutationinformation),]
|
||||
|
||||
# sanity check
|
||||
cat("Checking nrows in merged_df2_comp")
|
||||
if(nrow(merged_df2_comp) == (nrow(merged_df2) - na_count + 1)){
|
||||
cat("PASS: No. of rows match"
|
||||
,"\nDim of merged_df2_comp: "
|
||||
,"\nExpected no. of rows: ", nrow(merged_df2) - na_count + 1
|
||||
, "\nNo. of rows: ", nrow(merged_df2_comp)
|
||||
, "\nNo. of cols: ", ncol(merged_df2_comp))
|
||||
}else{
|
||||
cat("FAIL: No. of rows mismatch"
|
||||
,"\nExpected no. of rows: ", nrow(merged_df2) - na_count + 1
|
||||
,"\nGot no. of rows: ", nrow(merged_df2_comp))
|
||||
}
|
||||
|
||||
#########
|
||||
# merge 4b (merged_df3_comp): remove duplicate mutation information
|
||||
#########
|
||||
merged_df3_comp = merged_df2_comp[!duplicated(merged_df2_comp$mutationinformation),]
|
||||
|
||||
cat("Dim of merged_df3_comp: "
|
||||
, "\nNo. of rows: ", nrow(merged_df3_comp)
|
||||
, "\nNo. of cols: ", ncol(merged_df3_comp))
|
||||
|
||||
# alternate way of deriving merged_df3_comp
|
||||
foo = merged_df3[!is.na(merged_df3$AF),]
|
||||
# compare dfs: foo and merged_df3_com
|
||||
all.equal(foo, merged_df3)
|
||||
|
||||
summary(comparedf(foo, merged_df3))
|
||||
|
||||
# sanity check
|
||||
cat("Checking nrows in merged_df3_comp")
|
||||
if(nrow(merged_df3_comp) == nrow(merged_df3)){
|
||||
cat("NO NAs detected in merged_df3 in AF|OR cols"
|
||||
,"\nNo. of rows are identical: ", nrow(merged_df3))
|
||||
} else{
|
||||
if(nrow(merged_df3_comp) == nrow(merged_df3) - na_count_df3) {
|
||||
cat("PASS: NAs detected in merged_df3 in AF|OR cols"
|
||||
, "\nNo. of NAs: ", na_count_df3
|
||||
, "\nExpected no. of rows in merged_df3_comp: ", nrow(merged_df3) - na_count_df3
|
||||
, "\nGot no. of rows: ", nrow(merged_df3_comp))
|
||||
}
|
||||
}
|
||||
|
||||
#=============== end of combining df
|
||||
#*********************
|
||||
# writing 1 file in the style of a loop: merged_df3
|
||||
# print(output dir)
|
||||
#i = "merged_df3"
|
||||
#out_filename = paste0(i, ".csv")
|
||||
#outfile = paste0(outdir, "/", out_filename)
|
||||
|
||||
#cat("Writing output file: "
|
||||
# ,"\nFilename: ", out_filename
|
||||
# ,"\nPath: ", outdir)
|
||||
|
||||
#template: write.csv(merged_df3, "merged_df3.csv")
|
||||
#write.csv(get(i), outfile, row.names = FALSE)
|
||||
#cat("Finished writing: ", outfile
|
||||
# , "\nNo. of rows: ", nrow(get(i))
|
||||
# , "\nNo. of cols: ", ncol(get(i)))
|
||||
|
||||
#%% write_output files; all 4 files:
|
||||
outvars = c("merged_df2"
|
||||
, "merged_df3"
|
||||
, "merged_df2_comp"
|
||||
, "merged_df3_comp")
|
||||
|
||||
cat("Writing output files: "
|
||||
, "\nPath:", outdir)
|
||||
|
||||
for (i in outvars){
|
||||
# cat(i, "\n")
|
||||
out_filename = paste0(i, ".csv")
|
||||
# cat(out_filename, "\n")
|
||||
# cat("getting value of variable: ", get(i))
|
||||
outfile = paste0(outdir, "/", out_filename)
|
||||
# cat("Full output path: ", outfile, "\n")
|
||||
cat("Writing output file:"
|
||||
,"\nFilename: ", out_filename,"\n")
|
||||
write.csv(get(i), outfile, row.names = FALSE)
|
||||
cat("Finished writing: ", outfile
|
||||
, "\nNo. of rows: ", nrow(get(i))
|
||||
, "\nNo. of cols: ", ncol(get(i)), "\n")
|
||||
}
|
||||
|
||||
# alternate way to replace with implicit loop
|
||||
# FIXME
|
||||
#sapply(outvars, function(x, y) write.csv(get(outvars), paste0(outdir, "/", outvars, ".csv")))
|
||||
#*************************
|
||||
# clear variables
|
||||
rm(mcsm_data, gene_metadata, foo, drug, gene, gene_match, indir, merged_muts_u, meta_muts_u, na_count, df_ncols, outdir)
|
||||
rm(pos_count_check)
|
||||
#============================= end of script
|
||||
|
||||
Loading…
Add table
Add a link
Reference in a new issue