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added untracked files in scripts and dynamut

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Tanushree Tunstall 2022-01-04 12:26:54 +00:00
parent 00b84ccb1c
commit 3ab6a3dbc1
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scripts/functions/test_combining_dfs_plotting.R Normal file
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#!/usr/bin/env Rscript
# working dir and loading libraries
getwd()
setwd("~/git/LSHTM_analysis/scripts/functions/")
getwd()
# infile_params = paste0(outdir, "/" , tolower(gene), "_comb_afor.csv")
# infile_metadata = paste0(outdir, "/", tolower(gene), "_metadata")
#
#
# source("combining_dfs_plotting_func.R")
#
####################################################################
# in_file_params = "~/git/Data/streptomycin/output/gid_comb_afor.csv"
# in_file_metadata = "~/git/Data/streptomycin/output/gid_metadata.csv"
#
# all_plot_dfs = combining_dfs_plotting(df1_mcsm_comb = infile_params
# , df2_gene_metadata = infile_metadata
# , lig_dist_colname = 'ligand_distance'
# , lig_dist_cutoff = 10)
#
# merged_df2 = all_plot_dfs[[1]]
# merged_df3 = all_plot_dfs[[2]]
# merged_df2_comp = all_plot_dfs[[3]]
# merged_df3_comp = all_plot_dfs[[4]]
# merged_df2_lig = all_plot_dfs[[5]]
# merged_df3_lig = all_plot_dfs[[6]]
#
# bar_colnames = data.frame(colnames(merged_df2))
###########################################################
source("plotting_globals.R")
source("plotting_data.R")
source("combining_dfs_plotting.R")
#---------------------
# call: import_dirs()
#---------------------
gene = 'gid'
drug = 'streptomycin'
import_dirs(drug_name = drug, gene_name = gene)
#============================
# Input 1: plotting_data()
#============================
if (!exists("infile_params") && exists("gene")){
#if (!is.character(infile_params) && exists("gene")){
#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")
}
mcsm_comb_data = read.csv(infile_params, header = T)
#-------------------------------
# call function: plotting_data()
#-------------------------------
pd_df = plotting_data(df = mcsm_comb_data
, ligand_dist_colname = 'ligand_distance'
, lig_dist_cutoff = 10
my_df_u = pd_df[[2]]
#======================================
# Input 2: read <gene>_meta data.csv
#======================================
if (!exists("infile_metadata") && exists("gene")){
#if (!is.character(infile_params) && exists("gene")){{
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")
}
cat("\nReading meta data file:", infile_metadata)
gene_metadata <- read.csv(infile_metadata
, stringsAsFactors = F
, header = T)
#-----------------------------------------
# test function: combining_dfs_plotting()
#-----------------------------------------
all_plot_dfs = combining_dfs_plotting(my_df_u
, gene_metadata
, lig_dist_colname = 'ligand_distance'
, lig_dist_cutoff = 10)
merged_df2 = all_plot_dfs[[1]]
merged_df3 = all_plot_dfs[[2]]
merged_df2_comp = all_plot_dfs[[3]]
merged_df3_comp = all_plot_dfs[[4]]
merged_df2_lig = all_plot_dfs[[5]]
merged_df3_lig = all_plot_dfs[[6]]
merged_df2_comp_lig = all_plot_dfs[[7]]
merged_df3_comp_lig = all_plot_dfs[[8]]
########################################################################
# End of script
########################################################################