minor tidy up to check interactive graphs Rshiny
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6 changed files with 3 additions and 375 deletions
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#!/usr/bin/env Rscript
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library(ggplot2)
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library(tidyverse)
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library(data.table)
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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/"
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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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# read a sample file containing muts and prop
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###############################################
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df<- read.csv(file.choose())
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setDT(df)[, pos_count := .N, by = .(position)]
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foo = data.frame(df$position, df$pos_count)
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#snpsBYpos_df <- df %>%
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# group_by(position) %>%
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# summarize(snpsBYpos = mean(pos_count))
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# subset df without duplicates for position
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df2 = df[!duplicated(df$position)]
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##################################################################
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# ---------------------------------------
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# barplot for nssnps, coloured by aa prop
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# ---------------------------------------
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pos_colname = "position"
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aa_prop_colname = "mut_prop_water"
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aa_prop_colours = c("black", "blue")
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my_legname = "aa_prop: water"
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# call function
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aa_prop_bp(plotdf = df
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, position_colname = pos_colname
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, fill_colname = aa_prop_colname
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, fill_colours = aa_prop_cols
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, leg_name = my_legname)
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#===============================================================
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#!/usr/bin/env Rscript
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#########################################################
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# TASK: To calculate Allele Frequency and
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# Odds Ratio from master data
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#########################################################
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# load libraries
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#source("Header_TT.R")
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require("getopt", quietly = TRUE) # cmd parse arguments
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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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# load functions
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source("plotting_globals.R")
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source("mychisq_or.R")
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source("myaf_or_calcs.R")
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# cmd options + sensible defaults
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drug = "streptomycin"
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gene = "gid"
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# call function
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import_dirs(drug, gene)
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# input file 1: master data
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#in_filename_master = 'original_tanushree_data_v2.csv' #19K
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in_filename_master = 'mtb_gwas_meta_v6.csv' #35k
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infile_master = paste0(datadir, in_filename_master)
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cat(paste0('Reading infile1: raw data', ' ', infile_master) )
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# input file 2: gene associated meta data file to extract valid snps and add calcs to.
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# This is outfile_metadata from data_extraction.py
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in_filename_metadata = paste0(tolower(gene), '_metadata.csv')
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infile_metadata = paste0(outdir, '/', in_filename_metadata)
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cat(paste0('Reading input file 2 i.e gene associated metadata:', infile_metadata))
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# out_filename_af_or = paste0(tolower(gene), '_meta_data_with_AF_OR.csv')
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out_filename_af_or = paste0(tolower(gene), '_af_or.csv')
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outfile_af_or = paste0(outdir, '/', out_filename_af_or)
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cat(paste0('Output file with full path:', outfile_af_or))
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cat("master data:", infile_master)
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cat("gene data:", infile_metadata)
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dr_muts_col # comes from global (dr_mutations_<drug>)
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other_muts_col # comes from global (other_mutations_<drug>)
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#################################################
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my_afor ( infile_master
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, infile_metadata
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, outfile = outfile_af_or
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#, outfile = "FOO_TEST.csv"
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, drug
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, gene
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, idcol = "id"
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, dr_muts_col
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, other_muts_col
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)
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#!/usr/bin/env Rscript
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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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drug = "streptomycin"
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gene = "gid"
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source("plotting_data.R")
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infile = paste0("~/git/Data/", drug, "/output/", gene, "_comb_stab_struc_params.csv")
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infile_df = read.csv(infile)
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lig_dist = 5
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pd_df = plotting_data(infile_df
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, lig_dist_colname = 'ligand_distance'
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, lig_dist_cutoff = lig_dist)
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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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#=====================
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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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, label_categories = c("Destabilising", "Stabilising")
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, leg_position = "top")
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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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lig_dist = 10
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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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, yaxis_title = paste0("Number of nsSNPs\nLigand dist: <", lig_dist, "\u212b")
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#, bp_plot_title = "Sites < 10 Ang of ligand"
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)
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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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#!/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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#---------------------
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# call: import_dirs()
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#---------------------
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gene = 'gid'
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drug = 'streptomycin'
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import_dirs(drug_name = drug, gene_name = gene)
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#============================
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# Input 1: plotting_data()
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#============================
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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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mcsm_comb_data = read.csv(infile_params, header = T)
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#-------------------------------
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# call function: plotting_data()
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#-------------------------------
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pd_df = plotting_data(df = mcsm_comb_data
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, ligand_dist_colname = 'ligand_distance'
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, lig_dist_cutoff = 10
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my_df_u = pd_df[[2]]
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#======================================
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# Input 2: read <gene>_meta data.csv
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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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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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#-----------------------------------------
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# test function: combining_dfs_plotting()
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#-----------------------------------------
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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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merged_df2_comp_lig = all_plot_dfs[[7]]
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merged_df3_comp_lig = all_plot_dfs[[8]]
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########################################################################
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# End of script
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########################################################################
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#!/usr/bin/env Rscript
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getwd()
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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_globals.R")
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drug = "streptomycin"
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gene = "gid"
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import_dirs(drug_name = drug, gene_name = gene)
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#-------------------------------
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# test function: plotting_data()
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#-------------------------------
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source("plotting_data.R")
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infile_params = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
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mcsm_comb_data = read.csv(infile_params, header = T)
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pd_df = plotting_data(df = mcsm_comb_data
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, ligand_dist_colname = 'ligand_distance'
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, lig_dist_cutoff = 10)
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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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########################################################################
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# End of script
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########################################################################
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@ -5,10 +5,9 @@
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#########################################################
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# working dir and loading libraries
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting")
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getwd()
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#setwd("~/git/LSHTM_analysis/scripts/plotting")
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source("Header_TT.R")
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source("/home/tanu/git/LSHTM_analysis/scripts/plotting/Header_TT.R")
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#********************
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# cmd args passed
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@ -36,8 +35,7 @@ import_dirs(drug, gene)
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#---------------------------
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if (!exists("infile_params") && exists("gene")){
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#if (!is.character(infile_params) && exists("gene")){ # when running as cmd
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in_filename_params = paste0(tolower(gene), "_all_params.csv") #for pncA (and for gid finally) 10/09/21
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#in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
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in_filename_params = paste0(tolower(gene), "_all_params.csv")
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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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