updating script to sort out proper merging for plotting
This commit is contained in:
parent
064182d784
commit
e10ab6a7c6
1 changed files with 121 additions and 30 deletions
|
|
@ -23,40 +23,91 @@ getwd()
|
|||
setwd("~/git/LSHTM_analysis/scripts/plotting/")
|
||||
getwd()
|
||||
|
||||
require("getopt", quietly = TRUE) # cmd parse arguments
|
||||
|
||||
# load functions
|
||||
source("Header_TT.R")
|
||||
#require(data.table)
|
||||
#require(arsenal)
|
||||
#require(compare)
|
||||
#library(tidyverse)
|
||||
source("plotting_data.R")
|
||||
source("../functions/plotting_globals.R")
|
||||
source("../functions/plotting_data.R")
|
||||
|
||||
# should return the following dfs, directories and variables
|
||||
# my_df
|
||||
# my_df_u
|
||||
# my_df_u_lig
|
||||
# dup_muts
|
||||
#############################################################
|
||||
# command line args
|
||||
#********************
|
||||
# !!!FUTURE TODO!!!
|
||||
# Can pass additional params of output/plot dir by user.
|
||||
# Not strictly required for my workflow since it is optimised
|
||||
# to have a streamlined input/output flow without filename worries.
|
||||
#********************
|
||||
spec = matrix(c(
|
||||
"drug" ,"d", 1, "character",
|
||||
"gene" ,"g", 1, "character",
|
||||
"data" ,"f", 2, "character"
|
||||
), byrow = TRUE, ncol = 4)
|
||||
|
||||
cat("Directories imported:"
|
||||
, "\n===================="
|
||||
, "\ndatadir:", datadir
|
||||
, "\nindir:", indir
|
||||
, "\noutdir:", outdir
|
||||
, "\nplotdir:", plotdir)
|
||||
opt = getopt(spec)
|
||||
|
||||
cat("Variables imported:"
|
||||
, "\n====================="
|
||||
, "\ndrug:", drug
|
||||
, "\ngene:", gene
|
||||
, "\ngene_match:", gene_match
|
||||
, "\nAngstrom symbol:", angstroms_symbol
|
||||
, "\nNo. of duplicated muts:", dup_muts_nu
|
||||
, "\ndr_muts_col:", dr_muts_col
|
||||
, "\nother_muts_col:", other_muts_col
|
||||
, "\ndrtype_col:", resistance_col)
|
||||
#FIXME: detect if script running from cmd, then set these
|
||||
drug = opt$drug
|
||||
gene = opt$gene
|
||||
infile = opt$data
|
||||
|
||||
# hardcoding when not using cmd
|
||||
#drug = "streptomycin"
|
||||
#gene = "gid"
|
||||
|
||||
# clear excess variable
|
||||
rm(my_df, upos, dup_muts)
|
||||
if(is.null(drug)|is.null(gene)) {
|
||||
stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
|
||||
}
|
||||
|
||||
#########################################################
|
||||
# call functions with relevant args
|
||||
#***********************************
|
||||
# import_dirs(): returns
|
||||
# datadir
|
||||
# indir
|
||||
# outdir
|
||||
# plotdir
|
||||
# dr_muts_col
|
||||
# other_muts_col
|
||||
# resistance_col
|
||||
#***********************************
|
||||
import_dirs(drug, gene)
|
||||
#***********************************
|
||||
# plotting_data(): returns
|
||||
# my_df
|
||||
# my_df_u
|
||||
# my_df_u_lig
|
||||
# dup_muts
|
||||
#***********************************
|
||||
#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
|
||||
|
||||
if (!exists("infile") && exists("gene")){
|
||||
#if (!is.character(infile) && exists("gene")){
|
||||
#in_filename_params = paste0(tolower(gene), "_all_params.csv")
|
||||
#in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined for gid
|
||||
in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
|
||||
infile = paste0(outdir, "/", in_filename_params)
|
||||
cat("\nInput file not specified, assuming filename: ", infile, "\n")
|
||||
}
|
||||
|
||||
# Get the DFs out of plotting_data()
|
||||
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]]
|
||||
|
||||
cat(paste0("Directories imported:"
|
||||
, "\ndatadir:" , datadir
|
||||
, "\nindir:" , indir
|
||||
, "\noutdir:" , outdir
|
||||
, "\nplotdir:" , plotdir))
|
||||
|
||||
cat(paste0("\nVariables imported:"
|
||||
, "\ndrug:" , drug
|
||||
, "\ngene:" , gene
|
||||
, "\ngene match:" , gene_match
|
||||
, "\n"))
|
||||
#========================================================
|
||||
#===========
|
||||
# input
|
||||
|
|
@ -102,7 +153,6 @@ cat("Dim:", dim(gene_metadata))
|
|||
|
||||
table(gene_metadata$mutation_info)
|
||||
|
||||
|
||||
# counting NAs in AF, OR cols
|
||||
# or_mychisq
|
||||
if (identical(sum(is.na(my_df_u$or_mychisq))
|
||||
|
|
@ -157,6 +207,10 @@ cat(paste0("Merging dfs with NAs: big df (1-many relationship b/w id & mut)"
|
|||
, "\nMerging columns identified:"))
|
||||
print(merging_cols)
|
||||
|
||||
# using all common cols create confusion, so pick one!
|
||||
# merging_cols = merging_cols[[1]]
|
||||
merging_cols = 'mutationinformation'
|
||||
|
||||
# important checks!
|
||||
table(nchar(my_df_u$mutationinformation))
|
||||
table(nchar(my_df_u$wild_type))
|
||||
|
|
@ -170,6 +224,43 @@ merged_df2 = merge(x = gene_metadata
|
|||
, all.y = T)
|
||||
|
||||
cat("Dim of merged_df2: ", dim(merged_df2))
|
||||
|
||||
dup_cols = names(merged_df2)[grepl("\\.x$|\\.y$", names(merged_df2))]
|
||||
cat("\nNo. of duplicate cols:", length(dup_cols))
|
||||
check_df_cols = merged_df2[dup_cols]
|
||||
|
||||
identical(check_df_cols$wild_type.x, check_df_cols$wild_type.y)
|
||||
identical(check_df_cols$position.x, check_df_cols$position.y)
|
||||
identical(check_df_cols$mutant_type.x, check_df_cols$mutant_type.y)
|
||||
# False: because some of the ones with OR don't have mutation
|
||||
identical(check_df_cols$mutation.x, check_df_cols$mutation.y)
|
||||
|
||||
cols_to_drop = names(merged_df2)[grepl("\\.y",names(merged_df2))]
|
||||
cat("\nNo. of cols to drop:", length(cols_to_drop))
|
||||
|
||||
# subset
|
||||
merged_df2 = merged_df2[,!(names(merged_df2)%in%cols_to_drop)]
|
||||
|
||||
# rename the cols with '.x' suffix
|
||||
names(merged_df2)[grepl("\\.x$|\\.y$", names(merged_df2))]
|
||||
colnames(merged_df2) <- gsub("\\.x$", "", colnames(merged_df2))
|
||||
names(merged_df2)[grepl("\\.x$|\\.y$", names(merged_df2))]
|
||||
|
||||
#======================================================
|
||||
#-------------
|
||||
# DEBUG
|
||||
#-------------
|
||||
merged_df2_g = merged_df2[,!(names(merged_df2)%in%cols_to_drop)]
|
||||
|
||||
check_cols = colnames(merged_df2)[!colnames(merged_df2)%in%colnames(merged_df2_g)]
|
||||
if ( identical(check_cols, cols_to_drop) ){
|
||||
cat("\nPASS: cols identified have been successfully dropped"
|
||||
, "\nNo. of cols dropped: ", length(check_cols)
|
||||
, "\nNo. of cols in original df: ", ncol(merged_df2)
|
||||
, "\nNo. of cols in revised df: " , ncol(merged_df2_g))
|
||||
}
|
||||
|
||||
#======================================================
|
||||
head(merged_df2$position)
|
||||
|
||||
# sanity check
|
||||
|
|
@ -185,7 +276,7 @@ if(nrow(gene_metadata) == nrow(merged_df2)){
|
|||
, "\nFinding discrepancy")
|
||||
merged_muts_u = unique(merged_df2$mutationinformation)
|
||||
meta_muts_u = unique(gene_metadata$mutationinformation)
|
||||
# find the index where it differs
|
||||
# find the index where it differs
|
||||
unique(meta_muts_u[! meta_muts_u %in% merged_muts_u])
|
||||
quit()
|
||||
}
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue