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checked logo_multiple_muts.R with the new sourcing script for data

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Tanushree Tunstall 2021-06-24 16:43:23 +01:00
parent 71d874e350
commit e75cfd2665
6 changed files with 120 additions and 296 deletions
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89
scripts/plotting/logo_combined.R
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@ -3,95 +3,6 @@
# TASK: producing logo-type plot showing
# multiple muts per position coloured by aa property
#########################################################
#=======================================================================
# working dir and loading libraries
getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd()
source("Header_TT.R")
source("../functions/plotting_globals.R")
source("../functions/plotting_data.R")
source("../functions/combining_dfs_plotting.R")
###########################################################
# command line args
#********************
#drug = 'streptomycin'
#gene = 'gid'
#********************
# !!!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_file1" , "fa", 2, "character",
"data_file2" , "fb", 2, "character"
), byrow = TRUE, ncol = 4)
opt = getopt(spec)
#FIXME: detect if script running from cmd, then set these
drug = opt$drug
gene = opt$gene
infile_params = opt$data_file1
infile_metadata = opt$data_file2
if(is.null(drug)|is.null(gene)) {
stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
}
#===========
# input
#===========
#---------------------
# call: import_dirs()
#---------------------
import_dirs(drug_name = drug, gene_name = gene)
#---------------------------
# call: plotting_data()
#---------------------------
#if (!exists("infile_params") && exists("gene")){
if (!is.character(infile_params) && exists("gene")){ # when running as cmd
#in_filename_params = paste0(tolower(gene), "_all_params.csv")
in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
infile_params = paste0(outdir, "/", in_filename_params)
cat("\nInput file for mcsm comb data not specified, assuming filename: ", infile_params, "\n")
}
# Input 1: read <gene>_comb_afor.csv
cat("\nReading mcsm combined data file: ", infile_params)
mcsm_df = read.csv(infile_params, header = T)
pd_df = plotting_data(mcsm_df)
my_df_u = pd_df[[2]]
#--------------------------------
# call: combining_dfs_plotting()
#--------------------------------
#if (!exists("infile_metadata") && exists("gene")){
if (!is.character(infile_metadata) && exists("gene")){ # when running as cmd
in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid
infile_metadata = paste0(outdir, "/", in_filename_metadata)
cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n")
}
# Input 2: read <gene>_meta data.csv
cat("\nReading meta data file: ", infile_metadata)
gene_metadata <- read.csv(infile_metadata
, stringsAsFactors = F
, header = T)
all_plot_dfs = combining_dfs_plotting(my_df_u
, gene_metadata
, lig_dist_colname = 'ligand_distance'
, lig_dist_cutoff = 10)
merged_df3 = all_plot_dfs[[2]]
#===========
# output
#===========