87 lines
3.1 KiB
R
87 lines
3.1 KiB
R
# #!/usr/bin/env Rscript
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# working dir and loading libraries
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/functions/")
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getwd()
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# infile_params = paste0(outdir, "/" , tolower(gene), "_comb_afor.csv")
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# infile_metadata = paste0(outdir, "/", tolower(gene), "_metadata")
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#
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#
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# source("combining_dfs_plotting_func.R")
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#
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####################################################################
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# in_file_params = "~/git/Data/streptomycin/output/gid_comb_afor.csv"
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# in_file_metadata = "~/git/Data/streptomycin/output/gid_metadata.csv"
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#
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# all_plot_dfs = combining_dfs_plotting(df1_mcsm_comb = infile_params
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# , df2_gene_metadata = infile_metadata
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# , lig_dist_colname = 'ligand_distance'
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# , lig_dist_cutoff = 10)
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#
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# merged_df2 = all_plot_dfs[[1]]
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# merged_df3 = all_plot_dfs[[2]]
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# merged_df2_comp = all_plot_dfs[[3]]
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# merged_df3_comp = all_plot_dfs[[4]]
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# merged_df2_lig = all_plot_dfs[[5]]
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# merged_df3_lig = all_plot_dfs[[6]]
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#
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# bar_colnames = data.frame(colnames(merged_df2))
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###########################################################
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source("plotting_globals.R")
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source("plotting_data.R")
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source("combining_dfs_plotting.R")
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gene = 'gid'
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drug = 'streptomycin'
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#---------------------
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# call: import_dirs()
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#---------------------
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import_dirs(drug, gene)
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if (!exists("infile_params") && exists("gene")){
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#if (!is.character(infile_params) && exists("gene")){
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#in_filename_params = paste0(tolower(gene), "_all_params.csv")
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in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
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infile_params = paste0(outdir, "/", in_filename_params)
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cat("\nInput file for mcsm comb data not specified, assuming filename: ", infile_params, "\n")
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}
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if (!exists("infile_metadata") && exists("gene")){
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#if (!is.character(infile_params) && exists("gene")){{
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in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid
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infile_metadata = paste0(outdir, "/", in_filename_metadata)
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cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n")
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}
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#============================
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# Input 1: plotting_data()
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#============================
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#---------------------
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# call: plotting_data()
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#---------------------
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pd_df = plotting_data(infile_params)
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my_df = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
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#======================================
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# Input 2: read <gene>_meta data.csv
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#======================================
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cat("\nReading meta data file:", infile_metadata)
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gene_metadata <- read.csv(infile_metadata
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, stringsAsFactors = F
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, header = T)
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all_plot_dfs = combining_dfs_plotting(my_df_u
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, gene_metadata
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, lig_dist_colname = 'ligand_distance'
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, lig_dist_cutoff = 10)
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merged_df2 = all_plot_dfs[[1]]
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merged_df3 = all_plot_dfs[[2]]
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merged_df2_comp = all_plot_dfs[[3]]
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merged_df3_comp = all_plot_dfs[[4]]
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merged_df2_lig = all_plot_dfs[[5]]
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merged_df3_lig = all_plot_dfs[[6]]
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