diff --git a/scripts/functions/plotting_data.R b/scripts/functions/plotting_data.R index 73f450c..105abc8 100755 --- a/scripts/functions/plotting_data.R +++ b/scripts/functions/plotting_data.R @@ -103,9 +103,9 @@ cat("\nNo. of unique mutational positions:"); cat(length(upos), "\n") #=============================================== # extract mutations <10 Angstroms and symbol #=============================================== -table(my_df_u$ligand_distance_meta data.csv @@ -74,7 +78,10 @@ cat("\nReading meta data file:", infile_metadata) gene_metadata <- read.csv(infile_metadata , stringsAsFactors = F , header = T) - + +#----------------------------------------- +# test function: combining_dfs_plotting() +#----------------------------------------- all_plot_dfs = combining_dfs_plotting(my_df_u , gene_metadata , lig_dist_colname = 'ligand_distance' @@ -87,4 +94,7 @@ merged_df3_comp = all_plot_dfs[[4]] merged_df2_lig = all_plot_dfs[[5]] merged_df3_lig = all_plot_dfs[[6]] merged_df2_comp_lig = all_plot_dfs[[7]] -merged_df3_comp_lig = all_plot_dfs[[8]] \ No newline at end of file +merged_df3_comp_lig = all_plot_dfs[[8]] +######################################################################## +# End of script +######################################################################## diff --git a/scripts/functions/test_plotting_data.R b/scripts/functions/test_plotting_data.R index 9822d09..bb5ea3c 100644 --- a/scripts/functions/test_plotting_data.R +++ b/scripts/functions/test_plotting_data.R @@ -22,9 +22,14 @@ source("plotting_data.R") infile_params = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv" mcsm_comb_data = read.csv(infile_params, header = T) -pd_df = plotting_data(df = mcsm_comb_data, lig_dist_cutoff = 10) +pd_df = plotting_data(df = mcsm_comb_data + , ligand_dist_colname = 'ligand_distance' + , lig_dist_cutoff = 10) + my_df = pd_df[[1]] my_df_u = pd_df[[2]] my_df_u_lig = pd_df[[3]] dup_muts = pd_df[[4]] -#=============================================================== +######################################################################## +# End of script +######################################################################## \ No newline at end of file diff --git a/scripts/plotting/Header_TT.R b/scripts/plotting/Header_TT.R index bd21ed8..199031b 100755 --- a/scripts/plotting/Header_TT.R +++ b/scripts/plotting/Header_TT.R @@ -7,6 +7,8 @@ # install.packages("gplots", dependencies = TRUE) # library(gplots) #} +require(extrafont) + require("getopt", quietly = TRUE) # cmd parse arguments if (!require("tidyverse")) { diff --git a/scripts/plotting/basic_barplots.R b/scripts/plotting/basic_barplots.R index aaddce9..ef5a4dd 100755 --- a/scripts/plotting/basic_barplots.R +++ b/scripts/plotting/basic_barplots.R @@ -80,10 +80,10 @@ if (!exists("infile_params") && exists("gene")){ # Get the DFs out of plotting_data() pd_df = plotting_data(infile_params) -my_df = pd_df[[1]] +#my_df = pd_df[[1]] my_df_u = pd_df[[2]] -my_df_u_lig = pd_df[[3]] -dup_muts = pd_df[[4]] +#my_df_u_lig = pd_df[[3]] +#dup_muts = pd_df[[4]] cat(paste0("Directories imported:" , "\ndatadir:" , datadir diff --git a/scripts/plotting/corr_PS_LIG.R b/scripts/plotting/corr_PS_LIG.R index 30c3033..c566ca9 100644 --- a/scripts/plotting/corr_PS_LIG.R +++ b/scripts/plotting/corr_PS_LIG.R @@ -7,13 +7,13 @@ #======================================================================= # working dir and loading libraries getwd() -setwd("~/git/LSHTM_analysis/scripts/plotting/") +setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() source("Header_TT.R") require(cowplot) -source("combining_dfs_plotting.R") +source("../functions/combining_dfs_plotting.R") # should return the following dfs, directories and variables diff --git a/scripts/plotting/corr_data.R b/scripts/plotting/corr_data.R index 158c3c3..4d6847c 100644 --- a/scripts/plotting/corr_data.R +++ b/scripts/plotting/corr_data.R @@ -5,28 +5,67 @@ #======================================================================= # working dir and loading libraries getwd() -setwd("~/git/LSHTM_analysis/scripts/plotting/") +setwd("~/git/LSHTM_analysis/scripts/plotting") getwd() #source("Header_TT.R") -source("combining_dfs_plotting.R") -source("my_pairs_panel.R") # with lower panel turned off -# should return the following dfs, directories and variables +source("../functions/my_pairs_panel.R") # with lower panel turned off +source("../functions/plotting_globals.R") +source("../functions/plotting_data.R") +source("../functions/combining_dfs_plotting.R") +########################################################### +#=========== +# input +#=========== +#--------------------- +# call: import_dirs() +#--------------------- +import_dirs(drug, gene) + +#--------------------------- +# call: plotting_data() +#--------------------------- +#if (!exists("infile_params") && exists("gene")){ +if (!is.character(infile_params) && exists("gene")){ # when running as cmd + #in_filename_params = paste0(tolower(gene), "_all_params.csv") + in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid + infile_params = paste0(outdir, "/", in_filename_params) + cat("\nInput file for mcsm comb data not specified, assuming filename: ", infile_params, "\n") +} + +# Input 1: read _comb_afor.csv +cat("\nReading mcsm combined data file: ", infile_params) +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() + +#-------------------------------- +# call: combining_dfs_plotting() +#-------------------------------- +#if (!exists("infile_metadata") && exists("gene")){ +if (!is.character(infile_metadata) && exists("gene")){ # when running as cmd + in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid + infile_metadata = paste0(outdir, "/", in_filename_metadata) + cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n") +} + +# Input 2: read _meta data.csv +cat("\nReading meta data file: ", infile_metadata) + +gene_metadata <- read.csv(infile_metadata + , stringsAsFactors = F + , header = T) + +all_plot_dfs = combining_dfs_plotting(my_df_u + , gene_metadata + , lig_dist_colname = 'ligand_distance' + , lig_dist_cutoff = 10) + + + -# PS combined: -# 1) merged_df2 -# 2) merged_df2_comp -# 3) merged_df3 -# 4) merged_df3_comp -# LIG combined: -# 5) merged_df2_lig -# 6) merged_df2_comp_lig -# 7) merged_df3_lig -# 8) merged_df3_comp_lig -# 9) my_df_u -# 10) my_df_u_lig cat(paste0("Directories imported:" , "\ndatadir:", datadir diff --git a/scripts/plotting/logo_combined.R b/scripts/plotting/logo_combined.R old mode 100644 new mode 100755 index 4bc2a3f..1d14da0 --- a/scripts/plotting/logo_combined.R +++ b/scripts/plotting/logo_combined.R @@ -16,8 +16,32 @@ source("../functions/combining_dfs_plotting.R") ########################################################### # command line args #******************** -drug = 'streptomycin' -gene = 'gid' +#drug = 'streptomycin' +#gene = 'gid' +#******************** +# !!!FUTURE TODO!!! +# Can pass additional params of output/plot dir by user. +# Not strictly required for my workflow since it is optimised +# to have a streamlined input/output flow without filename worries. +#******************** +spec = matrix(c( + "drug" , "d", 1, "character", + "gene" , "g", 1, "character", + "data_file1" , "fa", 2, "character", + "data_file2" , "fb", 2, "character" +), byrow = TRUE, ncol = 4) + +opt = getopt(spec) + +#FIXME: detect if script running from cmd, then set these +drug = opt$drug +gene = opt$gene +infile_params = opt$data_file1 +infile_metadata = opt$data_file2 + +if(is.null(drug)|is.null(gene)) { + stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)") +} #=========== # input @@ -25,13 +49,13 @@ gene = 'gid' #--------------------- # call: import_dirs() #--------------------- -import_dirs(drug, gene) +import_dirs(drug_name = drug, gene_name = gene) #--------------------------- # call: plotting_data() #--------------------------- -if (!exists("infile_params") && exists("gene")){ - #if (!is.character(infile_params) && exists("gene")){ +#if (!exists("infile_params") && exists("gene")){ +if (!is.character(infile_params) && exists("gene")){ # when running as cmd #in_filename_params = paste0(tolower(gene), "_all_params.csv") in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid infile_params = paste0(outdir, "/", in_filename_params) @@ -39,21 +63,23 @@ if (!exists("infile_params") && exists("gene")){ } # Input 1: read _comb_afor.csv -pd_df = plotting_data(infile_params) -my_df_u = pd_df[[1]] # this forms one of the input for combining_dfs_plotting() +cat("\nReading mcsm combined data file: ", infile_params) +mcsm_df = read.csv(infile_params, header = T) +pd_df = plotting_data(mcsm_df) +my_df_u = pd_df[[2]] #-------------------------------- # call: combining_dfs_plotting() #-------------------------------- -if (!exists("infile_metadata") && exists("gene")){ - #if (!is.character(infile_params) && exists("gene")){{ +#if (!exists("infile_metadata") && exists("gene")){ +if (!is.character(infile_metadata) && exists("gene")){ # when running as cmd in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid infile_metadata = paste0(outdir, "/", in_filename_metadata) cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n") } # Input 2: read _meta data.csv -cat("\nReading meta data file:", infile_metadata) +cat("\nReading meta data file: ", infile_metadata) gene_metadata <- read.csv(infile_metadata , stringsAsFactors = F @@ -64,12 +90,8 @@ all_plot_dfs = combining_dfs_plotting(my_df_u , lig_dist_colname = 'ligand_distance' , lig_dist_cutoff = 10) -#merged_df2 = all_plot_dfs[[1]] -merged_df3 = all_plot_dfs[[2]] -#merged_df2_comp = all_plot_dfs[[3]] -#merged_df3_comp = all_plot_dfs[[4]] -#merged_df2_lig = all_plot_dfs[[5]] -#merged_df3_lig = all_plot_dfs[[6]] +merged_df3 = all_plot_dfs[[2]] + #=========== # output #=========== @@ -157,7 +179,7 @@ p0 = ggseqlogo(tab_mt , limits = c(0, max_mult_mut)) -p0 +#p0 # further customisation p1 = p0 + theme(axis.text.x = element_text(size = 16 @@ -167,7 +189,7 @@ p1 = p0 + theme(axis.text.x = element_text(size = 16 , axis.text.y = element_blank() , legend.position = "none") #, axis.text.y = element_text(size = 20)) -p1 +#p1 #============== # matrix for wild type @@ -204,7 +226,7 @@ p2 = ggseqlogo(tab_wt #theme_logo() + scale_x_discrete(breaks = 1:ncol(tab_wt) , labels = colnames(tab_wt)) -p2 +#p2 # further customise p3 = p2 + @@ -219,7 +241,7 @@ p3 = p2 + labs(x= "Wild-type Position") -p3 +#p3 #====================================================================== # logo with OR #======================================================================= @@ -302,7 +324,7 @@ logo_or = ggseqlogo(wide_df_or, method="custom", seq_type="aa") + ylab("my custo xlab("Position") + ylab("Odds Ratio") -logo_or +#logo_or ######################################################################## #============================= @@ -321,4 +343,4 @@ OutPlot2 = cowplot::plot_grid(logo_or, p1, p3 , label_size = 25) print(OutPlot2) -dev.off() +#dev.off() diff --git a/scripts/plotting/logo_multiple_muts.R b/scripts/plotting/logo_multiple_muts.R index bffd286..10cc496 100755 --- a/scripts/plotting/logo_multiple_muts.R +++ b/scripts/plotting/logo_multiple_muts.R @@ -65,7 +65,7 @@ if (!is.character(infile_params) && exists("gene")){ # when running as cmd cat("\nReading mcsm combined data file: ", infile_params) 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() @@ -172,22 +172,24 @@ p0 = ggseqlogo(tab_mt , seq_type = 'aa') + #ylab('my custom height') + theme(axis.text.x = element_blank()) + + theme(text=element_text(family="FreeSans"))+ theme_logo()+ scale_x_continuous(breaks = 1:ncol(tab_mt) , labels = colnames(tab_mt))+ scale_y_continuous( breaks = 1:max_mult_mut , limits = c(0, max_mult_mut)) -p0 +#p0 +cat('p0 done\n') # further customisation p1 = p0 + theme(legend.position = "none" , legend.title = element_blank() , legend.text = element_text(size = 20) , axis.text.x = element_text(size = 17, angle = 90) , axis.text.y = element_blank()) -p1 - +#p1 +cat('p0+p1 done\n') #============== # matrix for wild type # frequency of wild type by position @@ -218,14 +220,16 @@ p2 = ggseqlogo(tab_wt #, col_scheme = chemistry2 ) + #ylab('my custom height') + + theme(text=element_text(family="FreeSans"))+ theme(axis.text.x = element_blank() , axis.text.y = element_blank()) + theme_logo() + scale_x_continuous(breaks = 1:ncol(tab_wt) , labels = colnames(tab_wt)) -p2 +#p2 # further customise +cat('p2 done\n') p3 = p2 + theme(legend.position = "bottom" #, legend.title = element_blank() @@ -237,17 +241,20 @@ p3 = p2 + labs(x= "Position") -p3 +#p3 # Now combine using cowplot, which ensures the plots are aligned suppressMessages( require(cowplot) ) -plot_grid(p1, p3, ncol = 1, align = 'v') #+ +cat('p3 done\n') + +#plot_grid(p1, p3, ncol = 1, align = 'v') #+ +cat('p3+p2 done\n') #colour scheme #https://rdrr.io/cran/ggseqlogo/src/R/col_schemes.r -cat("Output plot:", plot_logo_multiple_muts) +cat("Output plot:", plot_logo_multiple_muts, "\n") svg(plot_logo_multiple_muts, width = 32, height = 10) @@ -257,4 +264,4 @@ OutPlot1 = cowplot::plot_grid(p1, p3 , rel_heights = c(3/4, 1/4)) print(OutPlot1) -dev.off() +#dev.off() diff --git a/scripts/plotting/logo_plot.R b/scripts/plotting/logo_plot.R index 8bf5cde..a11b2ca 100755 --- a/scripts/plotting/logo_plot.R +++ b/scripts/plotting/logo_plot.R @@ -68,7 +68,7 @@ if (!is.character(infile_params) && exists("gene")){ # when running as cmd cat("\nReading mcsm combined data file: ", infile_params) 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() diff --git a/scripts/plotting/merged_df3_short.csv b/scripts/plotting/merged_df3_short.csv deleted file mode 100644 index ad56364..0000000 --- a/scripts/plotting/merged_df3_short.csv +++ /dev/null @@ -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" diff --git a/scripts/plotting/my_pairs_panel.R b/scripts/plotting/my_pairs_panel.R deleted file mode 100644 index 8380f1f..0000000 --- a/scripts/plotting/my_pairs_panel.R +++ /dev/null @@ -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, ...) - } - } -} \ No newline at end of file diff --git a/scripts/plotting/running_plotting_scripts.txt b/scripts/plotting/running_plotting_scripts.txt index 08d4a25..060ab99 100644 --- a/scripts/plotting/running_plotting_scripts.txt +++ b/scripts/plotting/running_plotting_scripts.txt @@ -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 @@ -23,10 +23,61 @@ 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 Delete: dirs.R diff --git a/scripts/running_scripts b/scripts/running_scripts index 6d633e9..d1ca96b 100644 --- a/scripts/running_scripts +++ b/scripts/running_scripts @@ -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 -g @@ -67,5 +68,9 @@ USE THE BELOW from within the or_kinship_link.py script or something?! as part o #============================== mut_electrostatic_changes.py +# input now mcsm data, maps +# aa prop and then calculates +# checked +# TO DO: could turn to a function #============================== ./mut_electrostatic_changes.py -d -g