fixed cmd running script problem for logo plots
This commit is contained in:
parent
e822f9f690
commit
762b1a3931
14 changed files with 206 additions and 748 deletions
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@ -103,9 +103,9 @@ cat("\nNo. of unique mutational positions:"); cat(length(upos), "\n")
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#===============================================
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# extract mutations <10 Angstroms and symbol
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#===============================================
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table(my_df_u$ligand_distance<lig_dist_cutoff)
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table(my_df_u[[lig_dist_colname]] < lig_dist_cutoff)
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my_df_u_lig = my_df_u[my_df_u$ligand_distance <lig_dist_cutoff,]
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my_df_u_lig = my_df_u[my_df_u[[lig_dist_colname]] < lig_dist_cutoff,]
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cat(paste0("There are ", nrow(my_df_u_lig), " sites lying within 10\u212b of the ligand\n"))
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@ -41,9 +41,7 @@ drug = 'streptomycin'
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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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#============================
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# Input 1: plotting_data()
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#============================
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@ -56,7 +54,13 @@ if (!exists("infile_params") && exists("gene")){
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}
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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, lig_dist_cutoff = 10)
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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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@ -75,6 +79,9 @@ 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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@ -88,3 +95,6 @@ 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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@ -22,9 +22,14 @@ 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, lig_dist_cutoff = 10)
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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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########################################################################
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# End of script
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########################################################################
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@ -7,6 +7,8 @@
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# install.packages("gplots", dependencies = TRUE)
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# library(gplots)
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#}
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require(extrafont)
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require("getopt", quietly = TRUE) # cmd parse arguments
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if (!require("tidyverse")) {
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@ -80,10 +80,10 @@ if (!exists("infile_params") && exists("gene")){
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# Get the DFs out of plotting_data()
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pd_df = plotting_data(infile_params)
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my_df = pd_df[[1]]
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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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#my_df_u_lig = pd_df[[3]]
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#dup_muts = pd_df[[4]]
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cat(paste0("Directories imported:"
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, "\ndatadir:" , datadir
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@ -7,13 +7,13 @@
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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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setwd("~/git/LSHTM_analysis/scripts/plotting")
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getwd()
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source("Header_TT.R")
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require(cowplot)
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source("combining_dfs_plotting.R")
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source("../functions/combining_dfs_plotting.R")
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# should return the following dfs, directories and variables
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@ -5,28 +5,67 @@
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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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setwd("~/git/LSHTM_analysis/scripts/plotting")
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getwd()
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#source("Header_TT.R")
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source("combining_dfs_plotting.R")
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source("my_pairs_panel.R") # with lower panel turned off
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# should return the following dfs, directories and variables
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source("../functions/my_pairs_panel.R") # with lower panel turned off
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source("../functions/plotting_globals.R")
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source("../functions/plotting_data.R")
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source("../functions/combining_dfs_plotting.R")
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###########################################################
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#===========
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# input
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#===========
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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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#---------------------------
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# call: 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")){ # when running as cmd
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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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# Input 1: read <gene>_comb_afor.csv
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cat("\nReading mcsm combined data file: ", infile_params)
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mcsm_df = read.csv(infile_params, header = T)
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pd_df = plotting_data(mcsm_df)
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my_df_u = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
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#--------------------------------
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# call: combining_dfs_plotting()
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#--------------------------------
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#if (!exists("infile_metadata") && exists("gene")){
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if (!is.character(infile_metadata) && exists("gene")){ # when running as cmd
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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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# Input 2: read <gene>_meta data.csv
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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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# PS combined:
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# 1) merged_df2
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# 2) merged_df2_comp
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# 3) merged_df3
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# 4) merged_df3_comp
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# LIG combined:
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# 5) merged_df2_lig
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# 6) merged_df2_comp_lig
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# 7) merged_df3_lig
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# 8) merged_df3_comp_lig
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# 9) my_df_u
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# 10) my_df_u_lig
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cat(paste0("Directories imported:"
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, "\ndatadir:", datadir
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64
scripts/plotting/logo_combined.R
Normal file → Executable file
64
scripts/plotting/logo_combined.R
Normal file → Executable file
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@ -16,8 +16,32 @@ source("../functions/combining_dfs_plotting.R")
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###########################################################
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# command line args
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#********************
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drug = 'streptomycin'
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gene = 'gid'
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#drug = 'streptomycin'
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#gene = 'gid'
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#********************
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# !!!FUTURE TODO!!!
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# Can pass additional params of output/plot dir by user.
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# Not strictly required for my workflow since it is optimised
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# to have a streamlined input/output flow without filename worries.
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#********************
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spec = matrix(c(
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"drug" , "d", 1, "character",
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"gene" , "g", 1, "character",
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"data_file1" , "fa", 2, "character",
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"data_file2" , "fb", 2, "character"
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), byrow = TRUE, ncol = 4)
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opt = getopt(spec)
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#FIXME: detect if script running from cmd, then set these
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drug = opt$drug
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gene = opt$gene
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infile_params = opt$data_file1
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infile_metadata = opt$data_file2
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if(is.null(drug)|is.null(gene)) {
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stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
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}
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#===========
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# input
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@ -25,13 +49,13 @@ gene = 'gid'
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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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import_dirs(drug_name = drug, gene_name = gene)
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#---------------------------
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# call: 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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#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")
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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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@ -39,21 +63,23 @@ if (!exists("infile_params") && exists("gene")){
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}
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# Input 1: read <gene>_comb_afor.csv
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pd_df = plotting_data(infile_params)
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my_df_u = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
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cat("\nReading mcsm combined data file: ", infile_params)
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mcsm_df = read.csv(infile_params, header = T)
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pd_df = plotting_data(mcsm_df)
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my_df_u = pd_df[[2]]
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#--------------------------------
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# call: combining_dfs_plotting()
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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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#if (!exists("infile_metadata") && exists("gene")){
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if (!is.character(infile_metadata) && exists("gene")){ # when running as cmd
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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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# Input 2: read <gene>_meta data.csv
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cat("\nReading meta data file:", infile_metadata)
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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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@ -64,12 +90,8 @@ all_plot_dfs = combining_dfs_plotting(my_df_u
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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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#===========
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# output
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#===========
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@ -157,7 +179,7 @@ p0 = ggseqlogo(tab_mt
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, limits = c(0, max_mult_mut))
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p0
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#p0
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# further customisation
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p1 = p0 + theme(axis.text.x = element_text(size = 16
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@ -167,7 +189,7 @@ p1 = p0 + theme(axis.text.x = element_text(size = 16
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, axis.text.y = element_blank()
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, legend.position = "none")
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#, axis.text.y = element_text(size = 20))
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p1
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#p1
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#==============
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# matrix for wild type
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@ -204,7 +226,7 @@ p2 = ggseqlogo(tab_wt
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#theme_logo() +
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scale_x_discrete(breaks = 1:ncol(tab_wt)
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, labels = colnames(tab_wt))
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p2
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#p2
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# further customise
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p3 = p2 +
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@ -219,7 +241,7 @@ p3 = p2 +
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labs(x= "Wild-type Position")
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p3
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#p3
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#======================================================================
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# logo with OR
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#=======================================================================
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@ -302,7 +324,7 @@ logo_or = ggseqlogo(wide_df_or, method="custom", seq_type="aa") + ylab("my custo
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xlab("Position") +
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ylab("Odds Ratio")
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logo_or
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#logo_or
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########################################################################
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#=============================
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@ -321,4 +343,4 @@ OutPlot2 = cowplot::plot_grid(logo_or, p1, p3
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, label_size = 25)
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print(OutPlot2)
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dev.off()
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#dev.off()
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@ -65,7 +65,7 @@ if (!is.character(infile_params) && exists("gene")){ # when running as cmd
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cat("\nReading mcsm combined data file: ", infile_params)
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mcsm_df = read.csv(infile_params, header = T)
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pd_df = plotting_data(mcsm_df)
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my_df_u = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
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my_df_u = pd_df[[2]] # this forms one of the input for combining_dfs_plotting()
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#--------------------------------
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# call: combining_dfs_plotting()
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@ -172,22 +172,24 @@ p0 = ggseqlogo(tab_mt
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, seq_type = 'aa') +
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#ylab('my custom height') +
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theme(axis.text.x = element_blank()) +
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theme(text=element_text(family="FreeSans"))+
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theme_logo()+
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scale_x_continuous(breaks = 1:ncol(tab_mt)
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, labels = colnames(tab_mt))+
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scale_y_continuous( breaks = 1:max_mult_mut
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, limits = c(0, max_mult_mut))
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p0
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#p0
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cat('p0 done\n')
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# further customisation
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p1 = p0 + theme(legend.position = "none"
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, legend.title = element_blank()
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, legend.text = element_text(size = 20)
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, axis.text.x = element_text(size = 17, angle = 90)
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, axis.text.y = element_blank())
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p1
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#p1
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cat('p0+p1 done\n')
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#==============
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# matrix for wild type
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# frequency of wild type by position
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@ -218,14 +220,16 @@ p2 = ggseqlogo(tab_wt
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#, col_scheme = chemistry2
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) +
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#ylab('my custom height') +
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theme(text=element_text(family="FreeSans"))+
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theme(axis.text.x = element_blank()
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, axis.text.y = element_blank()) +
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theme_logo() +
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scale_x_continuous(breaks = 1:ncol(tab_wt)
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, labels = colnames(tab_wt))
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p2
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#p2
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# further customise
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cat('p2 done\n')
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p3 = p2 +
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theme(legend.position = "bottom"
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#, legend.title = element_blank()
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@ -237,17 +241,20 @@ p3 = p2 +
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labs(x= "Position")
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p3
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#p3
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# Now combine using cowplot, which ensures the plots are aligned
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suppressMessages( require(cowplot) )
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plot_grid(p1, p3, ncol = 1, align = 'v') #+
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cat('p3 done\n')
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#plot_grid(p1, p3, ncol = 1, align = 'v') #+
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cat('p3+p2 done\n')
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#colour scheme
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#https://rdrr.io/cran/ggseqlogo/src/R/col_schemes.r
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cat("Output plot:", plot_logo_multiple_muts)
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cat("Output plot:", plot_logo_multiple_muts, "\n")
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svg(plot_logo_multiple_muts, width = 32, height = 10)
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@ -257,4 +264,4 @@ OutPlot1 = cowplot::plot_grid(p1, p3
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, rel_heights = c(3/4, 1/4))
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print(OutPlot1)
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dev.off()
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#dev.off()
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@ -68,7 +68,7 @@ if (!is.character(infile_params) && exists("gene")){ # when running as cmd
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cat("\nReading mcsm combined data file: ", infile_params)
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mcsm_df = read.csv(infile_params, header = T)
|
||||
pd_df = plotting_data(mcsm_df)
|
||||
my_df_u = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
|
||||
my_df_u = pd_df[[2]] # this forms one of the input for combining_dfs_plotting()
|
||||
|
||||
#--------------------------------
|
||||
# call: combining_dfs_plotting()
|
||||
|
|
|
|||
|
|
@ -1,425 +0,0 @@
|
|||
"","mutation","mutationinformation","wild_type","position","mutant_type","mutation_info"
|
||||
"1","pnca_p.ala102pro","A102P","A",102,"P","other_mutations_pyrazinamide"
|
||||
"11","pnca_p.ala102arg","A102R","A",102,"R","other_mutations_pyrazinamide"
|
||||
"12","pnca_p.ala102thr","A102T","A",102,"T","dr_mutations_pyrazinamide"
|
||||
"15","pnca_p.ala102val","A102V","A",102,"V","other_mutations_pyrazinamide"
|
||||
"46","pnca_p.ala134asp","A134D","A",134,"D","other_mutations_pyrazinamide"
|
||||
"47","pnca_p.ala134gly","A134G","A",134,"G","other_mutations_pyrazinamide"
|
||||
"52","pnca_p.ala134pro","A134P","A",134,"P","other_mutations_pyrazinamide"
|
||||
"54","pnca_p.ala134thr","A134T","A",134,"T","other_mutations_pyrazinamide"
|
||||
"55","pnca_p.ala134val","A134V","A",134,"V","dr_mutations_pyrazinamide"
|
||||
"65","pnca_p.ala143asp","A143D","A",143,"D","dr_mutations_pyrazinamide"
|
||||
"68","pnca_p.ala143gly","A143G","A",143,"G","other_mutations_pyrazinamide"
|
||||
"73","pnca_p.ala143pro","A143P","A",143,"P","dr_mutations_pyrazinamide"
|
||||
"74","pnca_p.ala143thr","A143T","A",143,"T","dr_mutations_pyrazinamide"
|
||||
"76","pnca_p.ala143val","A143V","A",143,"V","other_mutations_pyrazinamide"
|
||||
"83","pnca_p.ala146glu","A146E","A",146,"E","dr_mutations_pyrazinamide"
|
||||
"93","pnca_p.ala146pro","A146P","A",146,"P","other_mutations_pyrazinamide"
|
||||
"96","pnca_p.ala146thr","A146T","A",146,"T","dr_mutations_pyrazinamide"
|
||||
"117","pnca_p.ala146val","A146V","A",146,"V","dr_mutations_pyrazinamide"
|
||||
"158","pnca_p.ala161gly","A161G","A",161,"G","other_mutations_pyrazinamide"
|
||||
"159","pnca_p.ala161val","A161V","A",161,"V","other_mutations_pyrazinamide"
|
||||
"160","pnca_p.ala171glu","A171E","A",171,"E","dr_mutations_pyrazinamide"
|
||||
"165","pnca_p.ala171pro","A171P","A",171,"P","dr_mutations_pyrazinamide"
|
||||
"167","pnca_p.ala171thr","A171T","A",171,"T","dr_mutations_pyrazinamide"
|
||||
"174","pnca_p.ala171val","A171V","A",171,"V","dr_mutations_pyrazinamide"
|
||||
"189","pnca_p.ala178pro","A178P","A",178,"P","other_mutations_pyrazinamide"
|
||||
"191","pnca_p.ala20pro","A20P","A",20,"P","other_mutations_pyrazinamide"
|
||||
"195","pnca_p.ala20ser","A20S","A",20,"S","other_mutations_pyrazinamide"
|
||||
"196","pnca_p.ala25val","A25V","A",25,"V","other_mutations_pyrazinamide"
|
||||
"199","pnca_p.ala28asp","A28D","A",28,"D","dr_mutations_pyrazinamide"
|
||||
"200","pnca_p.ala28thr","A28T","A",28,"T","other_mutations_pyrazinamide"
|
||||
"201","pnca_p.ala30val","A30V","A",30,"V","other_mutations_pyrazinamide"
|
||||
"203","pnca_p.ala3glu","A3E","A",3,"E","dr_mutations_pyrazinamide"
|
||||
"209","pnca_p.ala3pro","A3P","A",3,"P","dr_mutations_pyrazinamide"
|
||||
"212","pnca_p.ala46glu","A46E","A",46,"E","dr_mutations_pyrazinamide"
|
||||
"214","pnca_p.ala46pro","A46P","A",46,"P","dr_mutations_pyrazinamide"
|
||||
"216","pnca_p.ala46thr","A46T","A",46,"T","other_mutations_pyrazinamide"
|
||||
"218","pnca_p.ala46val","A46V","A",46,"V","dr_mutations_pyrazinamide"
|
||||
"233","pnca_p.ala79thr","A79T","A",79,"T","other_mutations_pyrazinamide"
|
||||
"235","pnca_p.ala79val","A79V","A",79,"V","other_mutations_pyrazinamide"
|
||||
"242","pnca_p.ala92gly","A92G","A",92,"G","other_mutations_pyrazinamide"
|
||||
"243","pnca_p.ala92pro","A92P","A",92,"P","other_mutations_pyrazinamide"
|
||||
"244","pnca_p.ala92val","A92V","A",92,"V","other_mutations_pyrazinamide"
|
||||
"245","pnca_p.cys138gly","C138G","C",138,"G","other_mutations_pyrazinamide"
|
||||
"247","pnca_p.cys138arg","C138R","C",138,"R","dr_mutations_pyrazinamide"
|
||||
"261","pnca_p.cys138ser","C138S","C",138,"S","dr_mutations_pyrazinamide"
|
||||
"262","pnca_p.cys138trp","C138W","C",138,"W","other_mutations_pyrazinamide"
|
||||
"263","pnca_p.cys138tyr","C138Y","C",138,"Y","dr_mutations_pyrazinamide"
|
||||
"268","pnca_p.cys14gly","C14G","C",14,"G","dr_mutations_pyrazinamide"
|
||||
"292","pnca_p.cys14arg","C14R","C",14,"R","dr_mutations_pyrazinamide"
|
||||
"378","pnca_p.cys14trp","C14W","C",14,"W","dr_mutations_pyrazinamide"
|
||||
"385","pnca_p.cys14tyr","C14Y","C",14,"Y","dr_mutations_pyrazinamide"
|
||||
"392","pnca_p.cys72gly","C72G","C",72,"G","other_mutations_pyrazinamide"
|
||||
"393","pnca_p.cys72arg","C72R","C",72,"R","dr_mutations_pyrazinamide"
|
||||
"404","pnca_p.cys72trp","C72W","C",72,"W","dr_mutations_pyrazinamide"
|
||||
"406","pnca_p.cys72tyr","C72Y","C",72,"Y","dr_mutations_pyrazinamide"
|
||||
"412","pnca_p.asp110his","D110H","D",110,"H","other_mutations_pyrazinamide"
|
||||
"413","pnca_p.asp126glu","D126E","D",126,"E","other_mutations_pyrazinamide"
|
||||
"417","pnca_p.asp129gly","D129G","D",129,"G","other_mutations_pyrazinamide"
|
||||
"419","pnca_p.asp129asn","D129N","D",129,"N","other_mutations_pyrazinamide"
|
||||
"421","pnca_p.asp129tyr","D129Y","D",129,"Y","other_mutations_pyrazinamide"
|
||||
"423","pnca_p.asp12ala","D12A","D",12,"A","dr_mutations_pyrazinamide"
|
||||
"484","pnca_p.asp12glu","D12E","D",12,"E","dr_mutations_pyrazinamide"
|
||||
"495","pnca_p.asp12gly","D12G","D",12,"G","dr_mutations_pyrazinamide"
|
||||
"506","pnca_p.asp12asn","D12N","D",12,"N","dr_mutations_pyrazinamide"
|
||||
"522","pnca_p.asp12tyr","D12Y","D",12,"Y","other_mutations_pyrazinamide"
|
||||
"523","pnca_p.asp136ala","D136A","D",136,"A","other_mutations_pyrazinamide"
|
||||
"524","pnca_p.asp136gly","D136G","D",136,"G","dr_mutations_pyrazinamide"
|
||||
"551","pnca_p.asp136asn","D136N","D",136,"N","dr_mutations_pyrazinamide"
|
||||
"563","pnca_p.asp136tyr","D136Y","D",136,"Y","dr_mutations_pyrazinamide"
|
||||
"574","pnca_p.asp145glu","D145E","D",145,"E","dr_mutations_pyrazinamide"
|
||||
"576","pnca_p.asp145tyr","D145Y","D",145,"Y","other_mutations_pyrazinamide"
|
||||
"577","pnca_p.asp33val","D33V","D",33,"V","other_mutations_pyrazinamide"
|
||||
"578","pnca_p.asp49ala","D49A","D",49,"A","dr_mutations_pyrazinamide"
|
||||
"592","pnca_p.asp49glu","D49E","D",49,"E","dr_mutations_pyrazinamide"
|
||||
"601","pnca_p.asp49gly","D49G","D",49,"G","dr_mutations_pyrazinamide"
|
||||
"634","pnca_p.asp49asn","D49N","D",49,"N","dr_mutations_pyrazinamide"
|
||||
"651","pnca_p.asp49tyr","D49Y","D",49,"Y","dr_mutations_pyrazinamide"
|
||||
"653","pnca_p.asp53glu","D53E","D",53,"E","other_mutations_pyrazinamide"
|
||||
"654","pnca_p.asp56glu","D56E","D",56,"E","other_mutations_pyrazinamide"
|
||||
"657","pnca_p.asp63ala","D63A","D",63,"A","dr_mutations_pyrazinamide"
|
||||
"678","pnca_p.asp63glu","D63E","D",63,"E","other_mutations_pyrazinamide"
|
||||
"680","pnca_p.asp63gly","D63G","D",63,"G","dr_mutations_pyrazinamide"
|
||||
"694","pnca_p.asp63his","D63H","D",63,"H","dr_mutations_pyrazinamide"
|
||||
"705","pnca_p.asp63val","D63V","D",63,"V","other_mutations_pyrazinamide"
|
||||
"706","pnca_p.asp63tyr","D63Y","D",63,"Y","other_mutations_pyrazinamide"
|
||||
"709","pnca_p.asp86gly","D86G","D",86,"G","other_mutations_pyrazinamide"
|
||||
"710","pnca_p.asp8ala","D8A","D",8,"A","dr_mutations_pyrazinamide"
|
||||
"716","pnca_p.asp8glu","D8E","D",8,"E","dr_mutations_pyrazinamide"
|
||||
"726","pnca_p.asp8gly","D8G","D",8,"G","dr_mutations_pyrazinamide"
|
||||
"744","pnca_p.asp8asn","D8N","D",8,"N","dr_mutations_pyrazinamide"
|
||||
"770","pnca_p.glu107asp","E107D","E",107,"D","other_mutations_pyrazinamide"
|
||||
"771","pnca_p.glu111asp","E111D","E",111,"D","other_mutations_pyrazinamide"
|
||||
"775","pnca_p.glu127asp","E127D","E",127,"D","other_mutations_pyrazinamide"
|
||||
"776","pnca_p.glu127val","E127V","E",127,"V","other_mutations_pyrazinamide"
|
||||
"777","pnca_p.glu15asp","E15D","E",15,"D","other_mutations_pyrazinamide"
|
||||
"778","pnca_p.glu15gly","E15G","E",15,"G","other_mutations_pyrazinamide"
|
||||
"784","pnca_p.glu173gly","E173G","E",173,"G","other_mutations_pyrazinamide"
|
||||
"788","pnca_p.glu174asp","E174D","E",174,"D","other_mutations_pyrazinamide"
|
||||
"789","pnca_p.glu174gly","E174G","E",174,"G","dr_mutations_pyrazinamide"
|
||||
"792","pnca_p.glu174lys","E174K","E",174,"K","other_mutations_pyrazinamide"
|
||||
"794","pnca_p.glu37val","E37V","E",37,"V","other_mutations_pyrazinamide"
|
||||
"795","pnca_p.phe106cys","F106C","F",106,"C","other_mutations_pyrazinamide"
|
||||
"796","pnca_p.phe106leu","F106L","F",106,"L","other_mutations_pyrazinamide"
|
||||
"802","pnca_p.phe106ser","F106S","F",106,"S","dr_mutations_pyrazinamide"
|
||||
"803","pnca_p.phe106val","F106V","F",106,"V","other_mutations_pyrazinamide"
|
||||
"805","pnca_p.phe13cys","F13C","F",13,"C","other_mutations_pyrazinamide"
|
||||
"809","pnca_p.phe13ile","F13I","F",13,"I","dr_mutations_pyrazinamide"
|
||||
"813","pnca_p.phe13leu","F13L","F",13,"L","dr_mutations_pyrazinamide"
|
||||
"825","pnca_p.phe13ser","F13S","F",13,"S","dr_mutations_pyrazinamide"
|
||||
"833","pnca_p.phe13val","F13V","F",13,"V","other_mutations_pyrazinamide"
|
||||
"835","pnca_p.phe58leu","F58L","F",58,"L","dr_mutations_pyrazinamide"
|
||||
"859","pnca_p.phe58ser","F58S","F",58,"S","dr_mutations_pyrazinamide"
|
||||
"867","pnca_p.phe58val","F58V","F",58,"V","other_mutations_pyrazinamide"
|
||||
"870","pnca_p.phe81cys","F81C","F",81,"C","other_mutations_pyrazinamide"
|
||||
"873","pnca_p.phe81ser","F81S","F",81,"S","other_mutations_pyrazinamide"
|
||||
"876","pnca_p.phe81val","F81V","F",81,"V","dr_mutations_pyrazinamide"
|
||||
"881","pnca_p.phe94cys","F94C","F",94,"C","dr_mutations_pyrazinamide"
|
||||
"890","pnca_p.phe94leu","F94L","F",94,"L","dr_mutations_pyrazinamide"
|
||||
"898","pnca_p.phe94ser","F94S","F",94,"S","dr_mutations_pyrazinamide"
|
||||
"903","pnca_p.phe94val","F94V","F",94,"V","other_mutations_pyrazinamide"
|
||||
"906","pnca_p.gly105asp","G105D","G",105,"D","dr_mutations_pyrazinamide"
|
||||
"911","pnca_p.gly105arg","G105R","G",105,"R","dr_mutations_pyrazinamide"
|
||||
"912","pnca_p.gly105val","G105V","G",105,"V","dr_mutations_pyrazinamide"
|
||||
"915","pnca_p.gly108glu","G108E","G",108,"E","other_mutations_pyrazinamide"
|
||||
"916","pnca_p.gly108arg","G108R","G",108,"R","dr_mutations_pyrazinamide"
|
||||
"925","pnca_p.gly124arg","G124R","G",124,"R","other_mutations_pyrazinamide"
|
||||
"926","pnca_p.gly124ser","G124S","G",124,"S","other_mutations_pyrazinamide"
|
||||
"927","pnca_p.gly132ala","G132A","G",132,"A","dr_mutations_pyrazinamide"
|
||||
"961","pnca_p.gly132asp","G132D","G",132,"D","dr_mutations_pyrazinamide"
|
||||
"981","pnca_p.gly132ser","G132S","G",132,"S","dr_mutations_pyrazinamide"
|
||||
"989","pnca_p.gly150asp","G150D","G",150,"D","other_mutations_pyrazinamide"
|
||||
"992","pnca_p.gly162ala","G162A","G",162,"A","other_mutations_pyrazinamide"
|
||||
"993","pnca_p.gly162asp","G162D","G",162,"D","dr_mutations_pyrazinamide"
|
||||
"1000","pnca_p.gly162arg","G162R","G",162,"R","other_mutations_pyrazinamide"
|
||||
"1006","pnca_p.gly162ser","G162S","G",162,"S","other_mutations_pyrazinamide"
|
||||
"1037","pnca_p.gly162val","G162V","G",162,"V","other_mutations_pyrazinamide"
|
||||
"1039","pnca_p.gly17ala","G17A","G",17,"A","other_mutations_pyrazinamide"
|
||||
"1041","pnca_p.gly17asp","G17D","G",17,"D","dr_mutations_pyrazinamide"
|
||||
"1054","pnca_p.gly17arg","G17R","G",17,"R","other_mutations_pyrazinamide"
|
||||
"1055","pnca_p.gly17ser","G17S","G",17,"S","other_mutations_pyrazinamide"
|
||||
"1062","pnca_p.gly23val","G23V","G",23,"V","dr_mutations_pyrazinamide"
|
||||
"1063","pnca_p.gly24asp","G24D","G",24,"D","dr_mutations_pyrazinamide"
|
||||
"1076","pnca_p.gly24arg","G24R","G",24,"R","dr_mutations_pyrazinamide"
|
||||
"1079","pnca_p.gly24ser","G24S","G",24,"S","other_mutations_pyrazinamide"
|
||||
"1080","pnca_p.gly24val","G24V","G",24,"V","other_mutations_pyrazinamide"
|
||||
"1081","pnca_p.gly55ser","G55S","G",55,"S","other_mutations_pyrazinamide"
|
||||
"1082","pnca_p.gly60asp","G60D","G",60,"D","other_mutations_pyrazinamide"
|
||||
"1090","pnca_p.gly78ala","G78A","G",78,"A","other_mutations_pyrazinamide"
|
||||
"1091","pnca_p.gly78cys","G78C","G",78,"C","dr_mutations_pyrazinamide"
|
||||
"1095","pnca_p.gly78arg","G78R","G",78,"R","other_mutations_pyrazinamide"
|
||||
"1097","pnca_p.gly78ser","G78S","G",78,"S","dr_mutations_pyrazinamide"
|
||||
"1104","pnca_p.gly78val","G78V","G",78,"V","dr_mutations_pyrazinamide"
|
||||
"1108","pnca_p.gly97ala","G97A","G",97,"A","other_mutations_pyrazinamide"
|
||||
"1110","pnca_p.gly97cys","G97C","G",97,"C","dr_mutations_pyrazinamide"
|
||||
"1140","pnca_p.gly97asp","G97D","G",97,"D","dr_mutations_pyrazinamide"
|
||||
"1193","pnca_p.gly97arg","G97R","G",97,"R","dr_mutations_pyrazinamide"
|
||||
"1195","pnca_p.gly97ser","G97S","G",97,"S","dr_mutations_pyrazinamide"
|
||||
"1214","pnca_p.gly97val","G97V","G",97,"V","other_mutations_pyrazinamide"
|
||||
"1216","pnca_p.his137asn","H137N","H",137,"N","other_mutations_pyrazinamide"
|
||||
"1218","pnca_p.his137pro","H137P","H",137,"P","dr_mutations_pyrazinamide"
|
||||
"1220","pnca_p.his137arg","H137R","H",137,"R","dr_mutations_pyrazinamide"
|
||||
"1226","pnca_p.his137tyr","H137Y","H",137,"Y","other_mutations_pyrazinamide"
|
||||
"1228","pnca_p.his43asp","H43D","H",43,"D","other_mutations_pyrazinamide"
|
||||
"1229","pnca_p.his43pro","H43P","H",43,"P","dr_mutations_pyrazinamide"
|
||||
"1231","pnca_p.his43tyr","H43Y","H",43,"Y","other_mutations_pyrazinamide"
|
||||
"1237","pnca_p.his51asp","H51D","H",51,"D","dr_mutations_pyrazinamide"
|
||||
"1282","pnca_p.his51asn","H51N","H",51,"N","dr_mutations_pyrazinamide"
|
||||
"1283","pnca_p.his51pro","H51P","H",51,"P","dr_mutations_pyrazinamide"
|
||||
"1293","pnca_p.his51gln","H51Q","H",51,"Q","dr_mutations_pyrazinamide"
|
||||
"1302","pnca_p.his51arg","H51R","H",51,"R","dr_mutations_pyrazinamide"
|
||||
"1384","pnca_p.his51tyr","H51Y","H",51,"Y","dr_mutations_pyrazinamide"
|
||||
"1394","pnca_p.his57asp","H57D","H",57,"D","dr_mutations_pyrazinamide"
|
||||
"1761","pnca_p.his57leu","H57L","H",57,"L","dr_mutations_pyrazinamide"
|
||||
"1766","pnca_p.his57pro","H57P","H",57,"P","dr_mutations_pyrazinamide"
|
||||
"1772","pnca_p.his57gln","H57Q","H",57,"Q","other_mutations_pyrazinamide"
|
||||
"1778","pnca_p.his57arg","H57R","H",57,"R","dr_mutations_pyrazinamide"
|
||||
"1815","pnca_p.his57tyr","H57Y","H",57,"Y","dr_mutations_pyrazinamide"
|
||||
"1825","pnca_p.his71asp","H71D","H",71,"D","dr_mutations_pyrazinamide"
|
||||
"1828","pnca_p.his71asn","H71N","H",71,"N","dr_mutations_pyrazinamide"
|
||||
"1829","pnca_p.his71pro","H71P","H",71,"P","other_mutations_pyrazinamide"
|
||||
"1833","pnca_p.his71gln","H71Q","H",71,"Q","dr_mutations_pyrazinamide"
|
||||
"1841","pnca_p.his71arg","H71R","H",71,"R","dr_mutations_pyrazinamide"
|
||||
"1862","pnca_p.his71tyr","H71Y","H",71,"Y","dr_mutations_pyrazinamide"
|
||||
"1911","pnca_p.his82asp","H82D","H",82,"D","dr_mutations_pyrazinamide"
|
||||
"1917","pnca_p.his82arg","H82R","H",82,"R","dr_mutations_pyrazinamide"
|
||||
"1930","pnca_p.his82tyr","H82Y","H",82,"Y","dr_mutations_pyrazinamide"
|
||||
"1931","pnca_p.ile133ser","I133S","I",133,"S","other_mutations_pyrazinamide"
|
||||
"1934","pnca_p.ile133thr","I133T","I",133,"T","dr_mutations_pyrazinamide"
|
||||
"1985","pnca_p.ile31ser","I31S","I",31,"S","dr_mutations_pyrazinamide"
|
||||
"1995","pnca_p.ile31thr","I31T","I",31,"T","other_mutations_pyrazinamide"
|
||||
"2021","pnca_p.ile52thr","I52T","I",52,"T","other_mutations_pyrazinamide"
|
||||
"2022","pnca_p.ile5ser","I5S","I",5,"S","dr_mutations_pyrazinamide"
|
||||
"2028","pnca_p.ile5thr","I5T","I",5,"T","dr_mutations_pyrazinamide"
|
||||
"2034","pnca_p.ile6leu","I6L","I",6,"L","other_mutations_pyrazinamide"
|
||||
"2213","pnca_p.ile6met","I6M","I",6,"M","dr_mutations_pyrazinamide"
|
||||
"2214","pnca_p.ile6ser","I6S","I",6,"S","dr_mutations_pyrazinamide"
|
||||
"2216","pnca_p.ile6thr","I6T","I",6,"T","dr_mutations_pyrazinamide"
|
||||
"2228","pnca_p.ile6val","I6V","I",6,"V","other_mutations_pyrazinamide"
|
||||
"2231","pnca_p.ile90ser","I90S","I",90,"S","dr_mutations_pyrazinamide"
|
||||
"2249","pnca_p.ile90thr","I90T","I",90,"T","other_mutations_pyrazinamide"
|
||||
"2253","pnca_p.lys48glu","K48E","K",48,"E","dr_mutations_pyrazinamide"
|
||||
"2266","pnca_p.lys48asn","K48N","K",48,"N","other_mutations_pyrazinamide"
|
||||
"2268","pnca_p.lys48gln","K48Q","K",48,"Q","other_mutations_pyrazinamide"
|
||||
"2273","pnca_p.lys48thr","K48T","K",48,"T","dr_mutations_pyrazinamide"
|
||||
"2302","pnca_p.lys96glu","K96E","K",96,"E","dr_mutations_pyrazinamide"
|
||||
"2316","pnca_p.lys96met","K96M","K",96,"M","other_mutations_pyrazinamide"
|
||||
"2320","pnca_p.lys96asn","K96N","K",96,"N","dr_mutations_pyrazinamide"
|
||||
"2325","pnca_p.lys96gln","K96Q","K",96,"Q","dr_mutations_pyrazinamide"
|
||||
"2335","pnca_p.lys96arg","K96R","K",96,"R","dr_mutations_pyrazinamide"
|
||||
"2362","pnca_p.lys96thr","K96T","K",96,"T","dr_mutations_pyrazinamide"
|
||||
"2387","pnca_p.leu116pro","L116P","L",116,"P","dr_mutations_pyrazinamide"
|
||||
"2404","pnca_p.leu116arg","L116R","L",116,"R","dr_mutations_pyrazinamide"
|
||||
"2411","pnca_p.leu116val","L116V","L",116,"V","dr_mutations_pyrazinamide"
|
||||
"2412","pnca_p.leu117arg","L117R","L",117,"R","other_mutations_pyrazinamide"
|
||||
"2414","pnca_p.leu120pro","L120P","L",120,"P","dr_mutations_pyrazinamide"
|
||||
"2471","pnca_p.leu120arg","L120R","L",120,"R","other_mutations_pyrazinamide"
|
||||
"2482","pnca_p.leu151ser","L151S","L",151,"S","dr_mutations_pyrazinamide"
|
||||
"2520","pnca_p.leu151val","L151V","L",151,"V","other_mutations_pyrazinamide"
|
||||
"2521","pnca_p.leu151trp","L151W","L",151,"W","other_mutations_pyrazinamide"
|
||||
"2522","pnca_p.leu156pro","L156P","L",156,"P","dr_mutations_pyrazinamide"
|
||||
"2526","pnca_p.leu156gln","L156Q","L",156,"Q","other_mutations_pyrazinamide"
|
||||
"2527","pnca_p.leu159pro","L159P","L",159,"P","dr_mutations_pyrazinamide"
|
||||
"2529","pnca_p.leu159arg","L159R","L",159,"R","dr_mutations_pyrazinamide"
|
||||
"2540","pnca_p.leu159val","L159V","L",159,"V","dr_mutations_pyrazinamide"
|
||||
"2542","pnca_p.leu172pro","L172P","L",172,"P","dr_mutations_pyrazinamide"
|
||||
"2575","pnca_p.leu172arg","L172R","L",172,"R","dr_mutations_pyrazinamide"
|
||||
"2580","pnca_p.leu182phe","L182F","L",182,"F","other_mutations_pyrazinamide"
|
||||
"2588","pnca_p.leu182ser","L182S","L",182,"S","dr_mutations_pyrazinamide"
|
||||
"2604","pnca_p.leu182trp","L182W","L",182,"W","other_mutations_pyrazinamide"
|
||||
"2606","pnca_p.leu19pro","L19P","L",19,"P","dr_mutations_pyrazinamide"
|
||||
"2615","pnca_p.leu19arg","L19R","L",19,"R","dr_mutations_pyrazinamide"
|
||||
"2620","pnca_p.leu19val","L19V","L",19,"V","other_mutations_pyrazinamide"
|
||||
"2624","pnca_p.leu27pro","L27P","L",27,"P","dr_mutations_pyrazinamide"
|
||||
"2646","pnca_p.leu27gln","L27Q","L",27,"Q","other_mutations_pyrazinamide"
|
||||
"2648","pnca_p.leu27arg","L27R","L",27,"R","other_mutations_pyrazinamide"
|
||||
"2651","pnca_p.leu35met","L35M","L",35,"M","other_mutations_pyrazinamide"
|
||||
"2652","pnca_p.leu35pro","L35P","L",35,"P","dr_mutations_pyrazinamide"
|
||||
"2662","pnca_p.leu35arg","L35R","L",35,"R","other_mutations_pyrazinamide"
|
||||
"2754","pnca_p.leu4ser","L4S","L",4,"S","dr_mutations_pyrazinamide"
|
||||
"2808","pnca_p.leu4val","L4V","L",4,"V","other_mutations_pyrazinamide"
|
||||
"2809","pnca_p.leu4trp","L4W","L",4,"W","dr_mutations_pyrazinamide"
|
||||
"2833","pnca_p.leu85pro","L85P","L",85,"P","dr_mutations_pyrazinamide"
|
||||
"2850","pnca_p.leu85arg","L85R","L",85,"R","dr_mutations_pyrazinamide"
|
||||
"2871","pnca_p.met175ile","M175I","M",175,"I","dr_mutations_pyrazinamide"
|
||||
"2880","pnca_p.met175lys","M175K","M",175,"K","dr_mutations_pyrazinamide"
|
||||
"2882","pnca_p.met175arg","M175R","M",175,"R","dr_mutations_pyrazinamide"
|
||||
"2884","pnca_p.met175thr","M175T","M",175,"T","dr_mutations_pyrazinamide"
|
||||
"2897","pnca_p.met175val","M175V","M",175,"V","dr_mutations_pyrazinamide"
|
||||
"2916","pnca_p.met1ile","M1I","M",1,"I","other_mutations_pyrazinamide"
|
||||
"2919","pnca_p.met1lys","M1K","M",1,"K","other_mutations_pyrazinamide"
|
||||
"2920","pnca_p.met1arg","M1R","M",1,"R","other_mutations_pyrazinamide"
|
||||
"2922","pnca_p.met1thr","M1T","M",1,"T","dr_mutations_pyrazinamide"
|
||||
"2948","pnca_p.asn112tyr","N112Y","N",112,"Y","other_mutations_pyrazinamide"
|
||||
"2949","pnca_p.asn118glu","N118E","N",118,"E","other_mutations_pyrazinamide"
|
||||
"2952","pnca_p.asn11ser","N11S","N",11,"S","other_mutations_pyrazinamide"
|
||||
"2953","pnca_p.asn149asp","N149D","N",149,"D","other_mutations_pyrazinamide"
|
||||
"2954","pnca_p.asn149ser","N149S","N",149,"S","other_mutations_pyrazinamide"
|
||||
"2955","pnca_p.asn149val","N149V","N",149,"V","other_mutations_pyrazinamide"
|
||||
"2957","pnca_p.pro115leu","P115L","P",115,"L","other_mutations_pyrazinamide"
|
||||
"2958","pnca_p.pro54ala","P54A","P",54,"A","other_mutations_pyrazinamide"
|
||||
"2960","pnca_p.pro54leu","P54L","P",54,"L","dr_mutations_pyrazinamide"
|
||||
"3004","pnca_p.pro54gln","P54Q","P",54,"Q","dr_mutations_pyrazinamide"
|
||||
"3010","pnca_p.pro54arg","P54R","P",54,"R","other_mutations_pyrazinamide"
|
||||
"3012","pnca_p.pro54ser","P54S","P",54,"S","other_mutations_pyrazinamide"
|
||||
"3022","pnca_p.pro62leu","P62L","P",62,"L","dr_mutations_pyrazinamide"
|
||||
"3042","pnca_p.pro62gln","P62Q","P",62,"Q","dr_mutations_pyrazinamide"
|
||||
"3043","pnca_p.pro62arg","P62R","P",62,"R","dr_mutations_pyrazinamide"
|
||||
"3046","pnca_p.pro62ser","P62S","P",62,"S","dr_mutations_pyrazinamide"
|
||||
"3052","pnca_p.pro62thr","P62T","P",62,"T","other_mutations_pyrazinamide"
|
||||
"3056","pnca_p.pro69leu","P69L","P",69,"L","dr_mutations_pyrazinamide"
|
||||
"3068","pnca_p.pro69gln","P69Q","P",69,"Q","other_mutations_pyrazinamide"
|
||||
"3069","pnca_p.pro69arg","P69R","P",69,"R","dr_mutations_pyrazinamide"
|
||||
"3073","pnca_p.pro69ser","P69S","P",69,"S","other_mutations_pyrazinamide"
|
||||
"3082","pnca_p.pro69thr","P69T","P",69,"T","other_mutations_pyrazinamide"
|
||||
"3084","pnca_p.pro77leu","P77L","P",77,"L","other_mutations_pyrazinamide"
|
||||
"3086","pnca_p.gln10glu","Q10E","Q",10,"E","other_mutations_pyrazinamide"
|
||||
"3088","pnca_p.gln10his","Q10H","Q",10,"H","dr_mutations_pyrazinamide"
|
||||
"3100","pnca_p.gln10leu","Q10L","Q",10,"L","other_mutations_pyrazinamide"
|
||||
"3101","pnca_p.gln10pro","Q10P","Q",10,"P","dr_mutations_pyrazinamide"
|
||||
"3430","pnca_p.gln10arg","Q10R","Q",10,"R","dr_mutations_pyrazinamide"
|
||||
"3488","pnca_p.gln122arg","Q122R","Q",122,"R","other_mutations_pyrazinamide"
|
||||
"3496","pnca_p.gln141pro","Q141P","Q",141,"P","dr_mutations_pyrazinamide"
|
||||
"3555","pnca_p.gln141arg","Q141R","Q",141,"R","other_mutations_pyrazinamide"
|
||||
"3560","pnca_p.arg121pro","R121P","R",121,"P","dr_mutations_pyrazinamide"
|
||||
"3562","pnca_p.arg121gln","R121Q","R",121,"Q","other_mutations_pyrazinamide"
|
||||
"3563","pnca_p.arg121trp","R121W","R",121,"W","other_mutations_pyrazinamide"
|
||||
"3564","pnca_p.arg123gly","R123G","R",123,"G","other_mutations_pyrazinamide"
|
||||
"3565","pnca_p.arg123pro","R123P","R",123,"P","dr_mutations_pyrazinamide"
|
||||
"3568","pnca_p.arg140gly","R140G","R",140,"G","dr_mutations_pyrazinamide"
|
||||
"3570","pnca_p.arg140his","R140H","R",140,"H","dr_mutations_pyrazinamide"
|
||||
"3571","pnca_p.arg140pro","R140P","R",140,"P","dr_mutations_pyrazinamide"
|
||||
"3575","pnca_p.arg140ser","R140S","R",140,"S","dr_mutations_pyrazinamide"
|
||||
"3581","pnca_p.arg148cys","R148C","R",148,"C","other_mutations_pyrazinamide"
|
||||
"3584","pnca_p.arg154gly","R154G","R",154,"G","dr_mutations_pyrazinamide"
|
||||
"3647","pnca_p.arg154ser","R154S","R",154,"S","other_mutations_pyrazinamide"
|
||||
"3650","pnca_p.arg154trp","R154W","R",154,"W","other_mutations_pyrazinamide"
|
||||
"3651","pnca_p.arg176cys","R176C","R",176,"C","other_mutations_pyrazinamide"
|
||||
"3652","pnca_p.arg2leu","R2L","R",2,"L","other_mutations_pyrazinamide"
|
||||
"3653","pnca_p.arg2pro","R2P","R",2,"P","other_mutations_pyrazinamide"
|
||||
"3654","pnca_p.arg2trp","R2W","R",2,"W","other_mutations_pyrazinamide"
|
||||
"3655","pnca_p.ser104gly","S104G","S",104,"G","dr_mutations_pyrazinamide"
|
||||
"3658","pnca_p.ser104ile","S104I","S",104,"I","other_mutations_pyrazinamide"
|
||||
"3659","pnca_p.ser104arg","S104R","S",104,"R","dr_mutations_pyrazinamide"
|
||||
"3690","pnca_p.ser164pro","S164P","S",164,"P","dr_mutations_pyrazinamide"
|
||||
"3700","pnca_p.ser179ile","S179I","S",179,"I","other_mutations_pyrazinamide"
|
||||
"3701","pnca_p.ser18pro","S18P","S",18,"P","dr_mutations_pyrazinamide"
|
||||
"3702","pnca_p.ser32gly","S32G","S",32,"G","other_mutations_pyrazinamide"
|
||||
"3703","pnca_p.ser32ile","S32I","S",32,"I","dr_mutations_pyrazinamide"
|
||||
"3705","pnca_p.ser59phe","S59F","S",59,"F","dr_mutations_pyrazinamide"
|
||||
"3708","pnca_p.ser59pro","S59P","S",59,"P","dr_mutations_pyrazinamide"
|
||||
"3745","pnca_p.ser59tyr","S59Y","S",59,"Y","other_mutations_pyrazinamide"
|
||||
"3746","pnca_p.ser65pro","S65P","S",65,"P","other_mutations_pyrazinamide"
|
||||
"3748","pnca_p.ser66leu","S66L","S",66,"L","other_mutations_pyrazinamide"
|
||||
"3755","pnca_p.ser66pro","S66P","S",66,"P","dr_mutations_pyrazinamide"
|
||||
"3758","pnca_p.ser67leu","S67L","S",67,"L","other_mutations_pyrazinamide"
|
||||
"3761","pnca_p.ser67pro","S67P","S",67,"P","dr_mutations_pyrazinamide"
|
||||
"3786","pnca_p.ser67thr","S67T","S",67,"T","other_mutations_pyrazinamide"
|
||||
"3787","pnca_p.ser67trp","S67W","S",67,"W","other_mutations_pyrazinamide"
|
||||
"3790","pnca_p.thr100ala","T100A","T",100,"A","other_mutations_pyrazinamide"
|
||||
"3795","pnca_p.thr100ile","T100I","T",100,"I","dr_mutations_pyrazinamide"
|
||||
"3806","pnca_p.thr100pro","T100P","T",100,"P","other_mutations_pyrazinamide"
|
||||
"3824","pnca_p.thr114met","T114M","T",114,"M","other_mutations_pyrazinamide"
|
||||
"3832","pnca_p.thr114pro","T114P","T",114,"P","dr_mutations_pyrazinamide"
|
||||
"3833","pnca_p.thr135ala","T135A","T",135,"A","other_mutations_pyrazinamide"
|
||||
"3836","pnca_p.thr135ile","T135I","T",135,"I","other_mutations_pyrazinamide"
|
||||
"3837","pnca_p.thr135pro","T135P","T",135,"P","dr_mutations_pyrazinamide"
|
||||
"3903","pnca_p.thr135ser","T135S","T",135,"S","other_mutations_pyrazinamide"
|
||||
"3904","pnca_p.thr142ala","T142A","T",142,"A","dr_mutations_pyrazinamide"
|
||||
"3921","pnca_p.thr142lys","T142K","T",142,"K","dr_mutations_pyrazinamide"
|
||||
"3927","pnca_p.thr142met","T142M","T",142,"M","dr_mutations_pyrazinamide"
|
||||
"3936","pnca_p.thr142pro","T142P","T",142,"P","dr_mutations_pyrazinamide"
|
||||
"3940","pnca_p.thr142arg","T142R","T",142,"R","other_mutations_pyrazinamide"
|
||||
"3941","pnca_p.thr153ile","T153I","T",153,"I","other_mutations_pyrazinamide"
|
||||
"3943","pnca_p.thr153pro","T153P","T",153,"P","other_mutations_pyrazinamide"
|
||||
"3944","pnca_p.thr160ala","T160A","T",160,"A","dr_mutations_pyrazinamide"
|
||||
"3960","pnca_p.thr160pro","T160P","T",160,"P","dr_mutations_pyrazinamide"
|
||||
"3976","pnca_p.thr160arg","T160R","T",160,"R","dr_mutations_pyrazinamide"
|
||||
"3988","pnca_p.thr167ile","T167I","T",167,"I","other_mutations_pyrazinamide"
|
||||
"3995","pnca_p.thr168ile","T168I","T",168,"I","other_mutations_pyrazinamide"
|
||||
"4000","pnca_p.thr168asn","T168N","T",168,"N","dr_mutations_pyrazinamide"
|
||||
"4001","pnca_p.thr168pro","T168P","T",168,"P","dr_mutations_pyrazinamide"
|
||||
"4004","pnca_p.thr168ser","T168S","T",168,"S","other_mutations_pyrazinamide"
|
||||
"4008","pnca_p.thr177pro","T177P","T",177,"P","other_mutations_pyrazinamide"
|
||||
"4013","pnca_p.thr22ala","T22A","T",22,"A","other_mutations_pyrazinamide"
|
||||
"4016","pnca_p.thr22pro","T22P","T",22,"P","other_mutations_pyrazinamide"
|
||||
"4017","pnca_p.thr47ala","T47A","T",47,"A","dr_mutations_pyrazinamide"
|
||||
"4037","pnca_p.thr47ile","T47I","T",47,"I","other_mutations_pyrazinamide"
|
||||
"4043","pnca_p.thr47asn","T47N","T",47,"N","other_mutations_pyrazinamide"
|
||||
"4044","pnca_p.thr47pro","T47P","T",47,"P","dr_mutations_pyrazinamide"
|
||||
"4050","pnca_p.thr61pro","T61P","T",61,"P","dr_mutations_pyrazinamide"
|
||||
"4057","pnca_p.thr61arg","T61R","T",61,"R","other_mutations_pyrazinamide"
|
||||
"4058","pnca_p.thr76ile","T76I","T",76,"I","dr_mutations_pyrazinamide"
|
||||
"4070","pnca_p.thr76pro","T76P","T",76,"P","dr_mutations_pyrazinamide"
|
||||
"4144","pnca_p.thr87met","T87M","T",87,"M","other_mutations_pyrazinamide"
|
||||
"4159","pnca_p.val125ala","V125A","V",125,"A","other_mutations_pyrazinamide"
|
||||
"4160","pnca_p.val125asp","V125D","V",125,"D","dr_mutations_pyrazinamide"
|
||||
"4184","pnca_p.val125phe","V125F","V",125,"F","other_mutations_pyrazinamide"
|
||||
"4196","pnca_p.val125gly","V125G","V",125,"G","dr_mutations_pyrazinamide"
|
||||
"4271","pnca_p.val128phe","V128F","V",128,"F","other_mutations_pyrazinamide"
|
||||
"4273","pnca_p.val128gly","V128G","V",128,"G","dr_mutations_pyrazinamide"
|
||||
"4297","pnca_p.val130ala","V130A","V",130,"A","dr_mutations_pyrazinamide"
|
||||
"4311","pnca_p.val130glu","V130E","V",130,"E","dr_mutations_pyrazinamide"
|
||||
"4313","pnca_p.val130gly","V130G","V",130,"G","dr_mutations_pyrazinamide"
|
||||
"4320","pnca_p.val130met","V130M","V",130,"M","other_mutations_pyrazinamide"
|
||||
"4324","pnca_p.val131phe","V131F","V",131,"F","dr_mutations_pyrazinamide"
|
||||
"4326","pnca_p.val131gly","V131G","V",131,"G","other_mutations_pyrazinamide"
|
||||
"4332","pnca_p.val139ala","V139A","V",139,"A","dr_mutations_pyrazinamide"
|
||||
"4379","pnca_p.val139gly","V139G","V",139,"G","dr_mutations_pyrazinamide"
|
||||
"4397","pnca_p.val139leu","V139L","V",139,"L","dr_mutations_pyrazinamide"
|
||||
"4414","pnca_p.val139met","V139M","V",139,"M","dr_mutations_pyrazinamide"
|
||||
"4431","pnca_p.val155ala","V155A","V",155,"A","dr_mutations_pyrazinamide"
|
||||
"4439","pnca_p.val155gly","V155G","V",155,"G","dr_mutations_pyrazinamide"
|
||||
"4452","pnca_p.val155leu","V155L","V",155,"L","dr_mutations_pyrazinamide"
|
||||
"4453","pnca_p.val155met","V155M","V",155,"M","dr_mutations_pyrazinamide"
|
||||
"4463","pnca_p.val157ala","V157A","V",157,"A","other_mutations_pyrazinamide"
|
||||
"4464","pnca_p.val157gly","V157G","V",157,"G","other_mutations_pyrazinamide"
|
||||
"4470","pnca_p.val157leu","V157L","V",157,"L","other_mutations_pyrazinamide"
|
||||
"4471","pnca_p.val163ala","V163A","V",163,"A","other_mutations_pyrazinamide"
|
||||
"4484","pnca_p.val163gly","V163G","V",163,"G","other_mutations_pyrazinamide"
|
||||
"4487","pnca_p.val163leu","V163L","V",163,"L","other_mutations_pyrazinamide"
|
||||
"4488","pnca_p.val180ala","V180A","V",180,"A","other_mutations_pyrazinamide"
|
||||
"4493","pnca_p.val180phe","V180F","V",180,"F","dr_mutations_pyrazinamide"
|
||||
"4507","pnca_p.val180gly","V180G","V",180,"G","dr_mutations_pyrazinamide"
|
||||
"4520","pnca_p.val180leu","V180L","V",180,"L","other_mutations_pyrazinamide"
|
||||
"4522","pnca_p.val183leu","V183L","V",183,"L","other_mutations_pyrazinamide"
|
||||
"4526","pnca_p.val21ala","V21A","V",21,"A","dr_mutations_pyrazinamide"
|
||||
"4532","pnca_p.val21gly","V21G","V",21,"G","dr_mutations_pyrazinamide"
|
||||
"4539","pnca_p.val21ile","V21I","V",21,"I","other_mutations_pyrazinamide"
|
||||
"4540","pnca_p.val44ala","V44A","V",44,"A","other_mutations_pyrazinamide"
|
||||
"4542","pnca_p.val44gly","V44G","V",44,"G","dr_mutations_pyrazinamide"
|
||||
"4555","pnca_p.val45ala","V45A","V",45,"A","other_mutations_pyrazinamide"
|
||||
"4556","pnca_p.val45glu","V45E","V",45,"E","other_mutations_pyrazinamide"
|
||||
"4559","pnca_p.val45gly","V45G","V",45,"G","dr_mutations_pyrazinamide"
|
||||
"4560","pnca_p.val73asp","V73D","V",73,"D","other_mutations_pyrazinamide"
|
||||
"4561","pnca_p.val7ala","V7A","V",7,"A","other_mutations_pyrazinamide"
|
||||
"4569","pnca_p.val7phe","V7F","V",7,"F","dr_mutations_pyrazinamide"
|
||||
"4573","pnca_p.val7gly","V7G","V",7,"G","dr_mutations_pyrazinamide"
|
||||
"4602","pnca_p.val7ile","V7I","V",7,"I","dr_mutations_pyrazinamide"
|
||||
"4603","pnca_p.val7leu","V7L","V",7,"L","dr_mutations_pyrazinamide"
|
||||
"4619","pnca_p.val93gly","V93G","V",93,"G","other_mutations_pyrazinamide"
|
||||
"4621","pnca_p.val93leu","V93L","V",93,"L","other_mutations_pyrazinamide"
|
||||
"4623","pnca_p.val9ala","V9A","V",9,"A","dr_mutations_pyrazinamide"
|
||||
"4630","pnca_p.val9gly","V9G","V",9,"G","dr_mutations_pyrazinamide"
|
||||
"4635","pnca_p.trp119cys","W119C","W",119,"C","dr_mutations_pyrazinamide"
|
||||
"4641","pnca_p.trp119gly","W119G","W",119,"G","other_mutations_pyrazinamide"
|
||||
"4643","pnca_p.trp119leu","W119L","W",119,"L","other_mutations_pyrazinamide"
|
||||
"4645","pnca_p.trp119arg","W119R","W",119,"R","dr_mutations_pyrazinamide"
|
||||
"4655","pnca_p.trp119ser","W119S","W",119,"S","dr_mutations_pyrazinamide"
|
||||
"4657","pnca_p.trp68cys","W68C","W",68,"C","dr_mutations_pyrazinamide"
|
||||
"4674","pnca_p.trp68gly","W68G","W",68,"G","dr_mutations_pyrazinamide"
|
||||
"4730","pnca_p.trp68leu","W68L","W",68,"L","dr_mutations_pyrazinamide"
|
||||
"4731","pnca_p.trp68arg","W68R","W",68,"R","dr_mutations_pyrazinamide"
|
||||
"4785","pnca_p.trp68ser","W68S","W",68,"S","dr_mutations_pyrazinamide"
|
||||
"4787","pnca_p.tyr103cys","Y103C","Y",103,"C","dr_mutations_pyrazinamide"
|
||||
"4803","pnca_p.tyr103asp","Y103D","Y",103,"D","other_mutations_pyrazinamide"
|
||||
"4841","pnca_p.tyr103his","Y103H","Y",103,"H","dr_mutations_pyrazinamide"
|
||||
"4851","pnca_p.tyr103ser","Y103S","Y",103,"S","dr_mutations_pyrazinamide"
|
||||
"4855","pnca_p.tyr34cys","Y34C","Y",34,"C","other_mutations_pyrazinamide"
|
||||
"4857","pnca_p.tyr34asp","Y34D","Y",34,"D","dr_mutations_pyrazinamide"
|
||||
"4904","pnca_p.tyr34ser","Y34S","Y",34,"S","dr_mutations_pyrazinamide"
|
||||
"4908","pnca_p.tyr41cys","Y41C","Y",41,"C","other_mutations_pyrazinamide"
|
||||
"4909","pnca_p.tyr41asp","Y41D","Y",41,"D","other_mutations_pyrazinamide"
|
||||
"4910","pnca_p.tyr64asp","Y64D","Y",64,"D","dr_mutations_pyrazinamide"
|
||||
"4915","pnca_p.tyr95asp","Y95D","Y",95,"D","other_mutations_pyrazinamide"
|
||||
|
|
|
@ -1,258 +0,0 @@
|
|||
my_pp = function (x, smooth = TRUE, scale = FALSE, density = TRUE, ellipses = TRUE,
|
||||
digits = 2, method = "pearson", pch = 20, lm = FALSE, cor = TRUE,
|
||||
jiggle = FALSE, factor = 2, hist.col = "cyan", show.points = TRUE,
|
||||
rug = TRUE, breaks = "Sturges", cex.cor = 1, wt = NULL, smoother = FALSE,
|
||||
stars = FALSE, ci = FALSE, alpha = 0.05, ...)
|
||||
{
|
||||
"panel.hist.density" <- function(x, ...) {
|
||||
usr <- par("usr")
|
||||
on.exit(par(usr))
|
||||
par(usr = c(usr[1], usr[2], 0, 1.5))
|
||||
tax <- table(x)
|
||||
if (length(tax) < 11) {
|
||||
breaks <- as.numeric(names(tax))
|
||||
y <- tax/max(tax)
|
||||
interbreak <- min(diff(breaks)) * (length(tax) -
|
||||
1)/41
|
||||
rect(breaks - interbreak, 0, breaks + interbreak,
|
||||
y, col = hist.col)
|
||||
}
|
||||
else {
|
||||
h <- hist(x, breaks = breaks, plot = FALSE)
|
||||
breaks <- h$breaks
|
||||
nB <- length(breaks)
|
||||
y <- h$counts
|
||||
y <- y/max(y)
|
||||
rect(breaks[-nB], 0, breaks[-1], y, col = hist.col)
|
||||
}
|
||||
if (density) {
|
||||
tryd <- try(d <- density(x, na.rm = TRUE, bw = "nrd",
|
||||
adjust = 1.2), silent = TRUE)
|
||||
if (!inherits(tryd, "try-error")) {
|
||||
d$y <- d$y/max(d$y)
|
||||
lines(d)
|
||||
}
|
||||
}
|
||||
if (rug)
|
||||
rug(x)
|
||||
}
|
||||
"panel.cor" <- function(x, y, prefix = "", ...) {
|
||||
usr <- par("usr")
|
||||
on.exit(par(usr))
|
||||
par(usr = c(0, 1, 0, 1))
|
||||
if (is.null(wt)) {
|
||||
r <- cor(x, y, use = "pairwise", method = method)
|
||||
}
|
||||
else {
|
||||
r <- cor.wt(data.frame(x, y), w = wt[, c(1:2)])$r[1,
|
||||
2]
|
||||
}
|
||||
txt <- format(c(round(r, digits), 0.123456789), digits = digits)[1]
|
||||
txt <- paste(prefix, txt, sep = "")
|
||||
if (stars) {
|
||||
pval <- r.test(sum(!is.na(x * y)), r)$p
|
||||
symp <- symnum(pval, corr = FALSE, cutpoints = c(0,
|
||||
0.001, 0.01, 0.05, 1), symbols = c("***", "**",
|
||||
"*", " "), legend = FALSE)
|
||||
txt <- paste0(txt, symp)
|
||||
}
|
||||
cex <- cex.cor * 0.8/(max(strwidth("0.12***"), strwidth(txt)))
|
||||
if (scale) {
|
||||
cex1 <- cex * abs(r)
|
||||
if (cex1 < 0.25)
|
||||
cex1 <- 0.25
|
||||
text(0.5, 0.5, txt, cex = cex1)
|
||||
}
|
||||
else {
|
||||
text(0.5, 0.5, txt, cex = cex)
|
||||
}
|
||||
}
|
||||
"panel.smoother" <- function(x, y, pch = par("pch"), col.smooth = "red",
|
||||
span = 2/3, iter = 3, ...) {
|
||||
xm <- mean(x, na.rm = TRUE)
|
||||
ym <- mean(y, na.rm = TRUE)
|
||||
xs <- sd(x, na.rm = TRUE)
|
||||
ys <- sd(y, na.rm = TRUE)
|
||||
r = cor(x, y, use = "pairwise", method = method)
|
||||
if (jiggle) {
|
||||
x <- jitter(x, factor = factor)
|
||||
y <- jitter(y, factor = factor)
|
||||
}
|
||||
if (smoother) {
|
||||
smoothScatter(x, y, add = TRUE, nrpoints = 0)
|
||||
}
|
||||
else {
|
||||
if (show.points)
|
||||
points(x, y, pch = pch, ...)
|
||||
}
|
||||
ok <- is.finite(x) & is.finite(y)
|
||||
if (any(ok)) {
|
||||
if (smooth & ci) {
|
||||
lml <- loess(y ~ x, degree = 1, family = "symmetric")
|
||||
tempx <- data.frame(x = seq(min(x, na.rm = TRUE),
|
||||
max(x, na.rm = TRUE), length.out = 47))
|
||||
pred <- predict(lml, newdata = tempx, se = TRUE)
|
||||
if (ci) {
|
||||
upperci <- pred$fit + confid * pred$se.fit
|
||||
lowerci <- pred$fit - confid * pred$se.fit
|
||||
polygon(c(tempx$x, rev(tempx$x)), c(lowerci,
|
||||
rev(upperci)), col = adjustcolor("light grey",
|
||||
alpha.f = 0.8), border = NA)
|
||||
}
|
||||
lines(tempx$x, pred$fit, col = col.smooth, ...)
|
||||
}
|
||||
else {
|
||||
if (smooth)
|
||||
lines(stats::lowess(x[ok], y[ok], f = span,
|
||||
iter = iter), col = col.smooth)
|
||||
}
|
||||
}
|
||||
if (ellipses)
|
||||
draw.ellipse(xm, ym, xs, ys, r, col.smooth = col.smooth,
|
||||
...)
|
||||
}
|
||||
"panel.lm" <- function(x, y, pch = par("pch"), col.lm = "red",
|
||||
...) {
|
||||
ymin <- min(y)
|
||||
ymax <- max(y)
|
||||
xmin <- min(x)
|
||||
xmax <- max(x)
|
||||
ylim <- c(min(ymin, xmin), max(ymax, xmax))
|
||||
xlim <- ylim
|
||||
if (jiggle) {
|
||||
x <- jitter(x, factor = factor)
|
||||
y <- jitter(y, factor = factor)
|
||||
}
|
||||
if (smoother) {
|
||||
smoothScatter(x, y, add = TRUE, nrpoints = 0)
|
||||
}
|
||||
else {
|
||||
if (show.points) {
|
||||
points(x, y, pch = pch, ylim = ylim, xlim = xlim,
|
||||
...)
|
||||
}
|
||||
}
|
||||
ok <- is.finite(x) & is.finite(y)
|
||||
if (any(ok)) {
|
||||
lml <- lm(y ~ x)
|
||||
if (ci) {
|
||||
tempx <- data.frame(x = seq(min(x, na.rm = TRUE),
|
||||
max(x, na.rm = TRUE), length.out = 47))
|
||||
pred <- predict.lm(lml, newdata = tempx, se.fit = TRUE)
|
||||
upperci <- pred$fit + confid * pred$se.fit
|
||||
lowerci <- pred$fit - confid * pred$se.fit
|
||||
polygon(c(tempx$x, rev(tempx$x)), c(lowerci,
|
||||
rev(upperci)), col = adjustcolor("light grey",
|
||||
alpha.f = 0.8), border = NA)
|
||||
}
|
||||
if (ellipses) {
|
||||
xm <- mean(x, na.rm = TRUE)
|
||||
ym <- mean(y, na.rm = TRUE)
|
||||
xs <- sd(x, na.rm = TRUE)
|
||||
ys <- sd(y, na.rm = TRUE)
|
||||
r = cor(x, y, use = "pairwise", method = method)
|
||||
draw.ellipse(xm, ym, xs, ys, r, col.smooth = col.lm,
|
||||
...)
|
||||
}
|
||||
abline(lml, col = col.lm, ...)
|
||||
}
|
||||
}
|
||||
"draw.ellipse" <- function(x = 0, y = 0, xs = 1, ys = 1,
|
||||
r = 0, col.smooth, add = TRUE, segments = 51, ...) {
|
||||
angles <- (0:segments) * 2 * pi/segments
|
||||
unit.circle <- cbind(cos(angles), sin(angles))
|
||||
if (!is.na(r)) {
|
||||
if (abs(r) > 0)
|
||||
theta <- sign(r)/sqrt(2)
|
||||
else theta = 1/sqrt(2)
|
||||
shape <- diag(c(sqrt(1 + r), sqrt(1 - r))) %*% matrix(c(theta,
|
||||
theta, -theta, theta), ncol = 2, byrow = TRUE)
|
||||
ellipse <- unit.circle %*% shape
|
||||
ellipse[, 1] <- ellipse[, 1] * xs + x
|
||||
ellipse[, 2] <- ellipse[, 2] * ys + y
|
||||
if (show.points)
|
||||
points(x, y, pch = 19, col = col.smooth, cex = 1.5)
|
||||
lines(ellipse, ...)
|
||||
}
|
||||
}
|
||||
"panel.ellipse" <- function(x, y, pch = par("pch"), col.smooth = "red",
|
||||
...) {
|
||||
segments = 51
|
||||
usr <- par("usr")
|
||||
on.exit(par(usr))
|
||||
par(usr = c(usr[1] - abs(0.05 * usr[1]), usr[2] + abs(0.05 *
|
||||
usr[2]), 0, 1.5))
|
||||
xm <- mean(x, na.rm = TRUE)
|
||||
ym <- mean(y, na.rm = TRUE)
|
||||
xs <- sd(x, na.rm = TRUE)
|
||||
ys <- sd(y, na.rm = TRUE)
|
||||
r = cor(x, y, use = "pairwise", method = method)
|
||||
if (jiggle) {
|
||||
x <- jitter(x, factor = factor)
|
||||
y <- jitter(y, factor = factor)
|
||||
}
|
||||
if (smoother) {
|
||||
smoothScatter(x, y, add = TRUE, nrpoints = 0)
|
||||
}
|
||||
else {
|
||||
if (show.points) {
|
||||
points(x, y, pch = pch, ...)
|
||||
}
|
||||
}
|
||||
angles <- (0:segments) * 2 * pi/segments
|
||||
unit.circle <- cbind(cos(angles), sin(angles))
|
||||
if (!is.na(r)) {
|
||||
if (abs(r) > 0)
|
||||
theta <- sign(r)/sqrt(2)
|
||||
else theta = 1/sqrt(2)
|
||||
shape <- diag(c(sqrt(1 + r), sqrt(1 - r))) %*% matrix(c(theta,
|
||||
theta, -theta, theta), ncol = 2, byrow = TRUE)
|
||||
ellipse <- unit.circle %*% shape
|
||||
ellipse[, 1] <- ellipse[, 1] * xs + xm
|
||||
ellipse[, 2] <- ellipse[, 2] * ys + ym
|
||||
points(xm, ym, pch = 19, col = col.smooth, cex = 1.5)
|
||||
if (ellipses)
|
||||
lines(ellipse, ...)
|
||||
}
|
||||
}
|
||||
old.par <- par(no.readonly = TRUE)
|
||||
on.exit(par(old.par))
|
||||
if (missing(cex.cor))
|
||||
cex.cor <- 1
|
||||
for (i in 1:ncol(x)) {
|
||||
if (is.character(x[[i]])) {
|
||||
x[[i]] <- as.numeric(as.factor(x[[i]]))
|
||||
colnames(x)[i] <- paste(colnames(x)[i], "*", sep = "")
|
||||
}
|
||||
}
|
||||
n.obs <- nrow(x)
|
||||
confid <- qt(1 - alpha/2, n.obs - 2)
|
||||
if (!lm) {
|
||||
if (cor) {
|
||||
pairs(x, diag.panel = panel.hist.density, upper.panel = panel.cor,
|
||||
#lower.panel = panel.smoother
|
||||
, lower.panel = NULL
|
||||
, pch = pch, ...)
|
||||
}
|
||||
else {
|
||||
pairs(x, diag.panel = panel.hist.density, upper.panel = panel.smoother,
|
||||
#lower.panel = panel.smoother
|
||||
, lower.panel = NULL
|
||||
, pch = pch, ...)
|
||||
}
|
||||
}
|
||||
else {
|
||||
if (!cor) {
|
||||
pairs(x, diag.panel = panel.hist.density, upper.panel = panel.lm,
|
||||
#lower.panel = panel.lm
|
||||
, lower.panel = NULL
|
||||
, pch = pch, ...)
|
||||
}
|
||||
else {
|
||||
pairs(x, diag.panel = panel.hist.density, upper.panel = panel.cor,
|
||||
#lower.panel = panel.lm
|
||||
, lower.panel = NULL
|
||||
, pch = pch, ...)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -15,7 +15,7 @@ sources:
|
|||
## stability_count_bp.R
|
||||
|
||||
outputs:
|
||||
##5 svgs in the plotdir
|
||||
## 5 svgs in the plotdir
|
||||
|
||||
note:
|
||||
-f flag has default if not supplied
|
||||
|
|
@ -23,9 +23,60 @@ sources:
|
|||
./basic_barplots.R -d streptomycin -g gid -f /home/tanu/gid_test_file.csv
|
||||
#-----------------------------------------------------------------------
|
||||
|
||||
#===================
|
||||
# log_plot.R
|
||||
#===================
|
||||
./logo_plot.R -d streptomycin -g gid
|
||||
|
||||
sources:
|
||||
## plotting_globals.R (previously dir.R)
|
||||
## plotting_data.R
|
||||
## combining_dfs_plotting.R
|
||||
|
||||
outputs: plotdir
|
||||
## 1 svg of OR for all positions
|
||||
|
||||
note:
|
||||
-fa flag has default if not supplied
|
||||
-fb flag has default if not supplied
|
||||
|
||||
#========================
|
||||
# ./logo_multiple_muts.R : FIXME,
|
||||
Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : polygon edge not found (new)
|
||||
https://stackoverflow.com/questions/34220883/error-in-grid-calll-textbounds-as-graphicsannotxlabel-xx-xy-polygon
|
||||
#========================
|
||||
./logo_multiple_muts.R -d streptomycin -g gid
|
||||
|
||||
sources:
|
||||
## plotting_globals.R (previously dir.R)
|
||||
## plotting_data.R
|
||||
## combining_dfs_plotting.R
|
||||
|
||||
outputs: plotdir
|
||||
## 1 svg of multiple muts for all positions > 1 muts (mutations + wt)
|
||||
|
||||
note:
|
||||
-fa flag has default if not supplied
|
||||
-fb flag has default if not supplied
|
||||
|
||||
#========================
|
||||
# ./logo_combined.R : FIXME,
|
||||
Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : polygon edge not found (new)
|
||||
https://stackoverflow.com/questions/34220883/error-in-grid-calll-textbounds-as-graphicsannotxlabel-xx-xy-polygon
|
||||
#========================
|
||||
|
||||
sources:
|
||||
## plotting_globals.R (previously dir.R)
|
||||
## plotting_data.R
|
||||
## combining_dfs_plotting.R
|
||||
|
||||
outputs: plotdir
|
||||
## 1 svg combined of OR logo plot + mulitple_muts i.e output from
|
||||
'logo_plots.R' + 'logo_multiple_muts.R'
|
||||
|
||||
note:
|
||||
-fa flag has default if not supplied
|
||||
-fb flag has default if not supplied
|
||||
|
||||
########################################################################
|
||||
# TODO
|
||||
|
|
|
|||
|
|
@ -36,6 +36,7 @@ In progress...
|
|||
#==============================
|
||||
# af_or_calcs.R: calculates af and or
|
||||
# opt defaults, uses sensible defaults
|
||||
# modified as funciton and checked!
|
||||
#==============================
|
||||
./af_or_calcs.R -d <drug> -g <gene>
|
||||
|
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|
@ -67,5 +68,9 @@ USE THE BELOW from within the or_kinship_link.py script or something?! as part o
|
|||
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#==============================
|
||||
mut_electrostatic_changes.py
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||||
# input now mcsm data, maps
|
||||
# aa prop and then calculates
|
||||
# checked
|
||||
# TO DO: could turn to a function
|
||||
#==============================
|
||||
./mut_electrostatic_changes.py -d <drug> -g <gene>
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue