103 lines
3.1 KiB
R
103 lines
3.1 KiB
R
setwd("~/git/LSHTM_analysis/scripts/functions/")
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getwd()
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#############################################################
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#===========================================
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# load functions, data, dirs, hardocded vars
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# that will be used in testing the functions
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#===========================================
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source("plotting_data.R")
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infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
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pd_df = plotting_data(infile)
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my_df = pd_df[[1]]
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my_df_u = pd_df[[2]]
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my_df_u_lig = pd_df[[3]]
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dup_muts = pd_df[[4]]
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source("plotting_globals.R")
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drug = "streptomycin"
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gene = "gid"
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import_dirs(drug, gene)
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#=====================
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# functions to test
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#=====================
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source("stability_count_bp.R")
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source("position_count_bp.R")
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##################################################################
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# ------------------------------
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# barplot for mscm stability
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# ------------------------------
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basic_bp_duet = paste0(tolower(gene), "_basic_barplot_PS.svg")
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plot_basic_bp_duet = paste0(plotdir,"/", basic_bp_duet)
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svg(plot_basic_bp_duet)
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print(paste0("plot filename:", basic_bp_duet))
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# function only
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stability_count_bp(plotdf = my_df_u
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, df_colname = "duet_outcome"
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, leg_title = "DUET outcome")
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dev.off()
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# ------------------------------
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# barplot for ligand affinity
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# ------------------------------
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basic_bp_ligand = paste0(tolower(gene), "_basic_barplot_LIG.svg")
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plot_basic_bp_ligand = paste0(plotdir, "/", basic_bp_ligand)
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svg(plot_basic_bp_ligand)
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print(paste0("plot filename:", basic_bp_ligand))
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# function only
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stability_count_bp(plotdf = my_df_u_lig
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, df_colname = "ligand_outcome"
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, leg_title = "Ligand outcome"
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, bp_plot_title = "Sites < 10 Ang of ligand")
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dev.off()
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# ------------------------------
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# barplot for foldX
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# ------------------------------
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basic_bp_foldx = paste0(tolower(gene), "_basic_barplot_foldx.svg")
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plot_basic_bp_foldx = paste0(plotdir,"/", basic_bp_foldx)
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svg(plot_basic_bp_foldx)
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print(paste0("plot filename:", plot_basic_bp_foldx))
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stability_count_bp(plotdf = my_df_u
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, df_colname = "foldx_outcome"
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, leg_title = "FoldX outcome")
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dev.off()
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#===============================================================
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# ------------------------------
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# barplot for nssnp site count: all
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# ------------------------------
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pos_count_duet = paste0(tolower(gene), "_position_count_PS.svg")
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plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
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svg(plot_pos_count_duet)
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print(paste0("plot filename:", plot_pos_count_duet))
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# function only
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site_snp_count_bp(plotdf = my_df_u
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, df_colname = "position")
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dev.off()
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# ------------------------------
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# barplot for nssnp site count: within 10 Ang
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# ------------------------------
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pos_count_ligand = paste0(tolower(gene), "_position_count_LIG.svg")
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plot_pos_count_ligand = paste0(plotdir, "/", pos_count_ligand)
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svg(plot_pos_count_ligand)
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print(paste0("plot filename:", plot_pos_count_ligand))
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# function only
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site_snp_count_bp(plotdf = my_df_u_lig
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, df_colname = "position")
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dev.off()
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#===============================================================
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