diff --git a/scripts/functions/bp_lineage.R b/scripts/functions/bp_lineage.R index 8585c82..8e1cf0a 100644 --- a/scripts/functions/bp_lineage.R +++ b/scripts/functions/bp_lineage.R @@ -1,6 +1,6 @@ ######################################## # Lineage barplot -# Lineage and nsSNP count barplot +# Lineage and SAV count barplot # Lineage Diversity barplot ######################################## @@ -28,7 +28,7 @@ lin_count_bp <- function( lf_data = lin_lf , leg_location = "top" , y_log10 = FALSE , y_scale_percent = FALSE - , y_label = c("Count", "SNP diversity") + , y_label = c("Count", "SAV diversity") , ... #, y_label = c("Count") ) { diff --git a/scripts/functions/bp_lineage_diversity.R b/scripts/functions/bp_lineage_diversity.R index 9fb6d66..efc1818 100644 --- a/scripts/functions/bp_lineage_diversity.R +++ b/scripts/functions/bp_lineage_diversity.R @@ -1,6 +1,6 @@ ######################################## # Lineage barplot -# Lineage and nsSNP count barplot +# Lineage and SAV count barplot # Lineage Diversity barplot ######################################## @@ -29,8 +29,8 @@ lin_count_bp_diversity <- function( lf_data = lin_wf , leg_location = "top" , y_log10 = FALSE , y_scale_percent = FALSE - #, y_label = c("Count", "SNP diversity") - , y_label = c("SNP diversity") + #, y_label = c("Count", "SAV diversity") + , y_label = c("SAV diversity") , bp_plot_title = "" , title_colour = "chocolate4" , subtitle_text = NULL diff --git a/scripts/functions/bp_subcolours.R b/scripts/functions/bp_subcolours.R index f89ba85..2465f0d 100755 --- a/scripts/functions/bp_subcolours.R +++ b/scripts/functions/bp_subcolours.R @@ -47,7 +47,7 @@ bp_stability_hmap <- function(plot_df = merged_df3 my_yaxts = 10, # y-axis text size my_pts = 10 # plot-title size , my_xlab = "Position" - , my_ylab = "No. of nsSNPs" + , my_ylab = "No. of SAVs" # Custom 2: x-axis: geom tiles ~ lig distance #, A_xvar_lig = T @@ -75,8 +75,8 @@ bp_stability_hmap <- function(plot_df = merged_df3 # stability values isolated to help with generating column called: 'group' my_grp = plot_df[[stability_colname]] - # cat( "\nLength of nsSNPs:", length(my_grp) - # , "\nLength of unique values for nsSNPs:", length(unique(my_grp)) ) + # cat( "\nLength of SAVs:", length(my_grp) + # , "\nLength of unique values for SAVs:", length(unique(my_grp)) ) # # Add col: 'group' plot_df$group = paste0(plot_df[[stability_outcome_colname]], "_", my_grp, sep = "") diff --git a/scripts/functions/ed_pfm_data.R b/scripts/functions/ed_pfm_data.R index 49bf9cd..757c993 100644 --- a/scripts/functions/ed_pfm_data.R +++ b/scripts/functions/ed_pfm_data.R @@ -40,7 +40,7 @@ DataED_PFM <- function(msaSeq_mut dash_control <- modifyList(dash_control_default, dash_control) ############################################ - # Data processing for logo plot for nsSNPS + # Data processing for logo plot for SAVS ########################################### cat("\nLength of MSA", length(msaSeq_mut)) diff --git a/scripts/functions/lineage_plot_data.R b/scripts/functions/lineage_plot_data.R index aadb872..444bb14 100644 --- a/scripts/functions/lineage_plot_data.R +++ b/scripts/functions/lineage_plot_data.R @@ -13,8 +13,8 @@ # For my case, this is called "lineage_labels" # This column has short labels like L1, L2, L3, etc. # if this is left empty, then the lineage_column_name will be used - # id_colname : sample-id column. Used to calculate SNP count - # snp_colname : SNP column. Used to calculate SNP diversity + # id_colname : sample-id column. Used to calculate SAV count + # snp_colname : SAV column. Used to calculate SAV diversity # RETURNS: List # WF and LF data for lineage-wise snp count and snp diversity @@ -142,7 +142,7 @@ lineage_plot_data <- function(plot_df lin_wf #---------------------- - # Add SNP diversity + # Add SAV diversity #---------------------- lin_wf$snp_diversity = lin_wf$num_snps_u/lin_wf$total_samples lin_wf @@ -150,7 +150,7 @@ lineage_plot_data <- function(plot_df #---------------------- # Add some formatting #---------------------- - # SNP diversity + # SAV diversity lin_wf$snp_diversity_f = round( (lin_wf$snp_diversity * 100), digits = 0) lin_wf$snp_diversity_f = paste0(lin_wf$snp_diversity_f, "%") diff --git a/scripts/functions/logoP_msa.R b/scripts/functions/logoP_msa.R index 86b8c72..f3108d0 100644 --- a/scripts/functions/logoP_msa.R +++ b/scripts/functions/logoP_msa.R @@ -366,7 +366,7 @@ LogoPlotMSA <- function(# unified_msa # <- not needed any more because we have ' } ##################################### - # Generating logo plots for nsSNPs + # Generating logo plots for SAVs ##################################### PlotlogolasL <- list() diff --git a/scripts/functions/logoP_snp.R b/scripts/functions/logoP_snp.R index 9be50d6..b83ac0d 100644 --- a/scripts/functions/logoP_snp.R +++ b/scripts/functions/logoP_snp.R @@ -14,8 +14,8 @@ # ...other params -# Returns: Logo plot from combined data containing all nsSNPs per position. -# Helps to see the overview of SNP diversity +# Returns: Logo plot from combined data containing all SAVs per position. +# Helps to see the overview of SAV diversity # TODO: SHINY # select/drop down: omit_snp_count @@ -37,7 +37,7 @@ LogoPlotSnps <- function(plot_df , omit_snp_count = c(0) # can be 1, 2, etc. , my_logo_col = "chemistry" , x_lab = "Position" - , y_lab = "nsSNP Count" + , y_lab = "SAV Count" , x_ats = 6 # text size , x_tangle = 90 # text angle , y_ats = 10 @@ -63,7 +63,7 @@ LogoPlotSnps <- function(plot_df omit_snp_count <- as.numeric(unlist(str_extract_all(omit_snp_count, regex("[0-9]+")))) } ############################################ - # Data processing for logo plot for nsSNPS + # Data processing for logo plot for SAVS ############################################ # Generate "ligand distance" colour map @@ -84,7 +84,7 @@ LogoPlotSnps <- function(plot_df max_mut = max(table(mutable_df[[x_axis_colname]])) # Subset Data as specified by user - cat("\nDisplaying nsSNP position frequency:\n") + cat("\nDisplaying SAV position frequency:\n") print(table(mutable_df$mut_pos_occurrence)) if ( (length(omit_snp_count) ==1) && (omit_snp_count == 0) ){ @@ -93,8 +93,8 @@ LogoPlotSnps <- function(plot_df max_mult_mut = max(table(my_data_snp[[x_axis_colname]])) if (debug) { cat("\nNo filtering requested:" - , "\nTotal no. of nsSNPs:", sum(table(mutable_df$mut_pos_occurrence)) - , "\nTotal no. of nsSNPs omitted:", sum(table(mutable_df$mut_pos_occurrence)[omit_snp_count]) + , "\nTotal no. of SAVs:", sum(table(mutable_df$mut_pos_occurrence)) + , "\nTotal no. of SAVs omitted:", sum(table(mutable_df$mut_pos_occurrence)[omit_snp_count]) , "\nDim of data:", dim(my_data_snp) , "\nNo. of positions:", length(u) , "\nMax no. of muts at any position:", max_mult_mut) @@ -109,15 +109,15 @@ LogoPlotSnps <- function(plot_df max_mult_mut = max(table(my_data_snp[[x_axis_colname]])) if (debug) { if (got_rows == exp_nrows) { - cat("\nPass: Position with the stated nsSNP frequency filtered:", omit_snp_count - , "\nTotal no. of nsSNPs:", sum(table(mutable_df$mut_pos_occurrence)) - , "\nTotal no. of nsSNPs omitted:", sum(table(mutable_df$mut_pos_occurrence)[omit_snp_count]) + cat("\nPass: Position with the stated SAV frequency filtered:", omit_snp_count + , "\nTotal no. of SAVs:", sum(table(mutable_df$mut_pos_occurrence)) + , "\nTotal no. of SAVs omitted:", sum(table(mutable_df$mut_pos_occurrence)[omit_snp_count]) , "\nDim of subsetted data:", dim(my_data_snp) , "\nNo. of positions:", length(u) , "\nMax no. of muts at any position:", max_mult_mut) } else { - cat("\nFAIL:Position with the stated nsSNP frequency COULD NOT be filtered..." + cat("\nFAIL:Position with the stated SAV frequency COULD NOT be filtered..." , "\nExpected:",exp_nrows , "\nGot:", got_rows ) } @@ -212,7 +212,7 @@ LogoPlotSnps <- function(plot_df position_mt = as.numeric(colnames(tab_mt)) position_wt = as.numeric(colnames(tab_wt)) ##################################### - # Generating logo plots for nsSNPs + # Generating logo plots for SAVs ##################################### #------------------- # Mutant logo plot diff --git a/scripts/functions/position_count_bp.R b/scripts/functions/position_count_bp.R index b4699b6..96cc994 100755 --- a/scripts/functions/position_count_bp.R +++ b/scripts/functions/position_count_bp.R @@ -1,7 +1,7 @@ #!/usr/bin/env Rscript ######################################################### -# TASK: function for barplot showing no. of sites with nsSNP +# TASK: function for barplot showing no. of sites with SAV # count ######################################################### # load libraries and functions @@ -11,7 +11,7 @@ library(dplyr) theme_set(theme_grey()) #================================================================= -# site_snp_count_bp(): barplots for no. of sites and nsSNP count +# site_snp_count_bp(): barplots for no. of sites and SAV count # input args ## df containing data to plot ## df column name containing site/position numbers @@ -31,7 +31,7 @@ site_snp_count_bp <- function (plotdf, axis_label_size = 10,#22 subtitle_size = 10,#20 geom_ls = 10, - xaxis_title = "Number of nsSNPs", + xaxis_title = "Number of SAVs", yaxis_title = "Number of Sites", title_colour = "chocolate4", subtitle_text = NULL, @@ -82,7 +82,7 @@ site_snp_count_bp <- function (plotdf, # sanity check if(tot_muts == nrow(plotdf)){ cat("\nPASS: total number of mutations match" - , "\nTotal no. of nsSNPs:", tot_muts) + , "\nTotal no. of SAVs:", tot_muts) } else{ cat("\nWARNING: total no. of muts = ", tot_muts , "\nExpected = ", nrow(plotdf)) @@ -106,13 +106,13 @@ site_snp_count_bp <- function (plotdf, , table(snpsBYpos_df$snpsBYpos) , "\n") - # calculating total no. of sites associated with nsSNPs + # calculating total no. of sites associated with SAVs tot_sites = sum(table(snpsBYpos_df$snpsBYpos)) # sanity check if(tot_sites == length(unique(plotdf$position))){ cat("\nPASS: total number of mutation sites match" - , "\nTotal no. of sites with nsSNPs:", tot_sites) + , "\nTotal no. of sites with SAVs:", tot_sites) } else{ cat("WARNING: total no. of sites = ", tot_sites , "\nExpected = ", length(unique(plotdf$position))) @@ -121,7 +121,7 @@ site_snp_count_bp <- function (plotdf, # FIXME: should really be legend title # but atm being using as plot title #my_leg_title - bp_plot_title = paste0("Total nsSNPs: ", tot_muts + bp_plot_title = paste0("Total SAVs: ", tot_muts , "\nTotal sites: ", tot_sites) #------------- diff --git a/scripts/functions/stability_count_bp.R b/scripts/functions/stability_count_bp.R index be872e2..d7fb439 100644 --- a/scripts/functions/stability_count_bp.R +++ b/scripts/functions/stability_count_bp.R @@ -22,7 +22,7 @@ stability_count_bp <- function(plotdf , lts = 10#20 # legend text size , ltis = 11#22 # label title size , geom_ls = 10 # geom_label size - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , bp_plot_title = "" , label_categories #= c("LEVEL1", "LEVEL2") , title_colour = "chocolate4" diff --git a/scripts/functions/tests/test_bp.R b/scripts/functions/tests/test_bp.R index 020a947..c53c015 100644 --- a/scripts/functions/tests/test_bp.R +++ b/scripts/functions/tests/test_bp.R @@ -62,7 +62,7 @@ lig_dist = 10 stability_count_bp(plotdf = my_df_u_lig , df_colname = "ligand_outcome" , leg_title = "Ligand outcome" - , yaxis_title = paste0("Number of nsSNPs\nLigand dist: <", lig_dist, "\u212b") + , yaxis_title = paste0("Number of SAVs\nLigand dist: <", lig_dist, "\u212b") #, bp_plot_title = "Sites < 10 Ang of ligand" ) diff --git a/scripts/functions/tests/test_bp_lineage.R b/scripts/functions/tests/test_bp_lineage.R index a198b82..b25b8dd 100644 --- a/scripts/functions/tests/test_bp_lineage.R +++ b/scripts/functions/tests/test_bp_lineage.R @@ -4,7 +4,7 @@ source ('get_plotting_dfs.R') source("../functions/bp_lineage.R") ######################################### -# Lineage and SNP count: lineage lf data +# Lineage and SAV count: lineage lf data ######################################### #========================= # Data: All lineages or @@ -35,7 +35,7 @@ lin_count_bp(lin_lf_plot = lin_lf , y_label = "Count") ############################################### -# Lineage SNP diversity count: lineage wf data +# Lineage SAV diversity count: lineage wf data ############################################### #========================= # Data: All lineages or @@ -59,4 +59,4 @@ lin_count_bp(lin_wf_plot = lin_wf , x_lab_angle = 90 , my_xats = 20 , y_scale_percent = T - , y_label = "SNP diversity") + , y_label = "SAV diversity") diff --git a/scripts/functions/tests/test_logo_plots.R b/scripts/functions/tests/test_logo_plots.R index c52c431..66e86ba 100644 --- a/scripts/functions/tests/test_logo_plots.R +++ b/scripts/functions/tests/test_logo_plots.R @@ -37,7 +37,7 @@ LP1<- LogoPlotCustomH (plot_df = merged_df3 ) ######################################## -# Logo plot showing nsSNPs by positions +# Logo plot showing SAVs by positions # wild-type and mutant aa # script: logoP_snp.R ######################################## @@ -48,7 +48,7 @@ LP2<- LogoPlotSnps(plot_df = merged_df3 , omit_snp_count = c(0)# can be 0,1, 2, etc.# DD , my_logo_col = "chemistry" #DD , x_lab = "Wild-type position" - , y_lab = "nsSNP count" + , y_lab = "SAV count" , x_ats = 10 , x_tangle = 90 , y_ats = 15 @@ -87,7 +87,7 @@ LP3<- LogoPlotMSA(unified_msa , x_axis_offset_filtered = 0.05 , y_axis_offset = 0.05 #, y_breaks = c(0, 2, 4, 6, 8, 10, 12) - , x_lab_mut = "nsSNP-position" + , x_lab_mut = "SAV-position" #, y_lab_mut , x_ats = 10 , x_tangle = 90 diff --git a/scripts/plotting/plotting_thesis/ORandSNP_results.R b/scripts/plotting/plotting_thesis/ORandSNP_results.R index 3eb7859..5ac71d9 100644 --- a/scripts/plotting/plotting_thesis/ORandSNP_results.R +++ b/scripts/plotting/plotting_thesis/ORandSNP_results.R @@ -85,7 +85,7 @@ foo2 = foo[foo$ligand_distance<10,] table(foo2$ligand_outcome) ############################# -# wide plots SNP +# wide plots SAV # DRUG length(aa_pos_drug); aa_pos_drug drug = foo[foo$position%in%aa_pos_drug,] diff --git a/scripts/plotting/plotting_thesis/alr/alr_ORandSNP_results.R b/scripts/plotting/plotting_thesis/alr/alr_ORandSNP_results.R index 3227f91..a875cba 100644 --- a/scripts/plotting/plotting_thesis/alr/alr_ORandSNP_results.R +++ b/scripts/plotting/plotting_thesis/alr/alr_ORandSNP_results.R @@ -76,7 +76,7 @@ foo2 = foo[foo$ligand_distance<10,] table(foo2$ligand_outcome) ############################# -# wide plots SNP +# wide plots SAV # DRUG length(aa_pos_drug); aa_pos_drug drug = foo[foo$position%in%aa_pos_drug,] diff --git a/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist.R b/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist.R index 19a412f..d416528 100644 --- a/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist.R +++ b/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist.R @@ -41,7 +41,7 @@ my_yals = 13 # y axis label size my_lls = 13 # legend label size d_lab_size = 5 #=============================== -# lineage sample and SNP count +# lineage sample and SAV count #=============================== lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']] , all_lineages = F @@ -58,7 +58,7 @@ lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']] , my_xals = my_xals # x axis label size , my_yals = my_yals # y axis label size , my_lls = my_lls # legend label size - , bar_col_labels = c("nsSNPs", "Total Samples") + , bar_col_labels = c("SAVs", "Total Samples") , bar_col_values = c("grey50", "gray75") , bar_leg_name = "" , leg_location = "top" @@ -68,7 +68,7 @@ lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']] ) lin_countP #=============================== -# lineage SNP diversity count +# lineage SAV diversity count #=============================== lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']] , x_categ = "sel_lineages" @@ -87,8 +87,8 @@ lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']] , y_log10 = F , y_scale_percent = F , leg_location = "top" - , y_label = "Percent" #"SNP diversity" - , bp_plot_title = "nsSNP diversity" + , y_label = "Percent" #"SAV diversity" + , bp_plot_title = "SAV diversity" , title_colour = "black" #"chocolate4" , subtitle_text = NULL , sts = 10 diff --git a/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist_layout.R b/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist_layout.R index 7144093..d093aeb 100644 --- a/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist_layout.R +++ b/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist_layout.R @@ -1,5 +1,5 @@ #!/usr/bin/env Rscript -source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist.R") +source("/home/sethp/git/LSHTM_analysis/scripts/plotting/plotting_thesis/alr/alr_lineage_bp_dist.R") ########################################### # TASK: generate plots for lineage diff --git a/scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R b/scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R index e75e8d8..6466a8b 100644 --- a/scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R +++ b/scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R @@ -65,7 +65,7 @@ mLigP = stability_count_bp(plotdf = df3_lig , df_colname = "ligand_outcome" #, leg_title = "mCSM-lig" #, bp_plot_title = paste(common_bp_title, "ligand") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nLig" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -113,7 +113,7 @@ if (tolower(gene)%in%geneL_ppi2){ #, label_categories = labels_ppi2 #, bp_plot_title = paste(common_bp_title, "PP-interface") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nPPI2" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -138,7 +138,7 @@ if (tolower(gene)%in%geneL_na){ #, label_categories = #, bp_plot_title = paste(common_bp_title, "Dist to NA") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nNA" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -162,7 +162,7 @@ common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol) posC_lig = site_snp_count_bp(plotdf = df3_lig , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -180,7 +180,7 @@ posC_lig if (tolower(gene)%in%geneL_ppi2){ posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -199,7 +199,7 @@ if (tolower(gene)%in%geneL_ppi2){ if (tolower(gene)%in%geneL_na){ posC_nca = site_snp_count_bp(plotdf = df3_na , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -217,7 +217,7 @@ if (tolower(gene)%in%geneL_na){ #------------------------------ posC_all = site_snp_count_bp(plotdf = df3 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "All mutations sites" @@ -233,7 +233,7 @@ consurfP = stability_count_bp(plotdf = df3 , df_colname = "consurf_outcome" #, leg_title = "ConSurf" #, label_categories = labels_consurf - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "top" , subtitle_text = "ConSurf" , bar_fill_values = consurf_colours_no_isd # from globals @@ -262,7 +262,7 @@ duetP = stability_count_bp(plotdf = df3 , df_colname = "duet_outcome" , leg_title = "mCSM-DUET" #, label_categories = labels_duet - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-DUET" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -331,7 +331,7 @@ proveanP = stability_count_bp(plotdf = df3 , df_colname = "provean_outcome" #, leg_title = "PROVEAN" #, label_categories = labels_provean - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" # top , subtitle_text = "PROVEAN" , bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep diff --git a/scripts/plotting/plotting_thesis/embb/basic_barplots_embb.R b/scripts/plotting/plotting_thesis/embb/basic_barplots_embb.R index 7eec863..9898fb0 100644 --- a/scripts/plotting/plotting_thesis/embb/basic_barplots_embb.R +++ b/scripts/plotting/plotting_thesis/embb/basic_barplots_embb.R @@ -68,7 +68,7 @@ mLigP = stability_count_bp(plotdf = df3_lig , df_colname = "ligand_outcome" #, leg_title = "mCSM-lig" #, bp_plot_title = paste(common_bp_title, "ligand") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nLig" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -116,7 +116,7 @@ if (tolower(gene)%in%geneL_ppi2){ #, label_categories = labels_ppi2 #, bp_plot_title = paste(common_bp_title, "PP-interface") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nPPI2" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -141,7 +141,7 @@ if (tolower(gene)%in%geneL_na){ #, label_categories = #, bp_plot_title = paste(common_bp_title, "Dist to NA") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nNA" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -165,7 +165,7 @@ common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol) posC_lig = site_snp_count_bp(plotdf = df3_lig , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -183,7 +183,7 @@ posC_lig if (tolower(gene)%in%geneL_ppi2){ posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -202,7 +202,7 @@ if (tolower(gene)%in%geneL_ppi2){ if (tolower(gene)%in%geneL_na){ posC_nca = site_snp_count_bp(plotdf = df3_na , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -220,7 +220,7 @@ if (tolower(gene)%in%geneL_na){ #------------------------------ posC_all = site_snp_count_bp(plotdf = df3 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "All mutations sites" @@ -235,7 +235,7 @@ consurfP = stability_count_bp(plotdf = df3 , df_colname = "consurf_outcome" #, leg_title = "ConSurf" #, label_categories = labels_consurf - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "top" , subtitle_text = "ConSurf" , bar_fill_values = consurf_colours # from globals @@ -264,7 +264,7 @@ duetP = stability_count_bp(plotdf = df3 , df_colname = "duet_outcome" , leg_title = "mCSM-DUET" #, label_categories = labels_duet - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-DUET" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -333,7 +333,7 @@ proveanP = stability_count_bp(plotdf = df3 , df_colname = "provean_outcome" #, leg_title = "PROVEAN" #, label_categories = labels_provean - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" # top , subtitle_text = "PROVEAN" , bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep diff --git a/scripts/plotting/plotting_thesis/embb/embb_ORandSNP_results.R b/scripts/plotting/plotting_thesis/embb/embb_ORandSNP_results.R index 4716963..e563807 100644 --- a/scripts/plotting/plotting_thesis/embb/embb_ORandSNP_results.R +++ b/scripts/plotting/plotting_thesis/embb/embb_ORandSNP_results.R @@ -78,7 +78,7 @@ foo2 = foo[foo$ligand_distance<10,] table(foo2$ligand_outcome) ############################# -# wide plots SNP +# wide plots SAV # DRUG length(aa_pos_drug); aa_pos_drug drug = foo[foo$position%in%aa_pos_drug,] diff --git a/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R b/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R index add5194..61e8688 100644 --- a/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R +++ b/scripts/plotting/plotting_thesis/gid/basic_barplots_gid.R @@ -67,7 +67,7 @@ mLigP = stability_count_bp(plotdf = df3_lig , df_colname = "ligand_outcome" #, leg_title = "mCSM-lig" #, bp_plot_title = paste(common_bp_title, "ligand") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nLig" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -115,7 +115,7 @@ if (tolower(gene)%in%geneL_ppi2){ #, label_categories = labels_ppi2 #, bp_plot_title = paste(common_bp_title, "PP-interface") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nPPI2" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -140,7 +140,7 @@ if (tolower(gene)%in%geneL_na){ #, label_categories = #, bp_plot_title = paste(common_bp_title, "Dist to NA") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nNA" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -164,7 +164,7 @@ common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol) posC_lig = site_snp_count_bp(plotdf = df3_lig , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -182,7 +182,7 @@ posC_lig if (tolower(gene)%in%geneL_ppi2){ posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -201,7 +201,7 @@ if (tolower(gene)%in%geneL_ppi2){ if (tolower(gene)%in%geneL_na){ posC_nca = site_snp_count_bp(plotdf = df3_na , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -219,7 +219,7 @@ if (tolower(gene)%in%geneL_na){ #------------------------------ posC_all = site_snp_count_bp(plotdf = df3 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "All mutations sites" @@ -234,7 +234,7 @@ consurfP = stability_count_bp(plotdf = df3 , df_colname = "consurf_outcome" #, leg_title = "ConSurf" #, label_categories = labels_consurf - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "top" , subtitle_text = "ConSurf" , bar_fill_values = consurf_colours # from globals @@ -263,7 +263,7 @@ duetP = stability_count_bp(plotdf = df3 , df_colname = "duet_outcome" , leg_title = "mCSM-DUET" #, label_categories = labels_duet - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-DUET" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -332,7 +332,7 @@ proveanP = stability_count_bp(plotdf = df3 , df_colname = "provean_outcome" #, leg_title = "PROVEAN" #, label_categories = labels_provean - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" # top , subtitle_text = "PROVEAN" , bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep diff --git a/scripts/plotting/plotting_thesis/gid/gid_ORandSNP_results.R b/scripts/plotting/plotting_thesis/gid/gid_ORandSNP_results.R index 2c072a2..6c15d8c 100644 --- a/scripts/plotting/plotting_thesis/gid/gid_ORandSNP_results.R +++ b/scripts/plotting/plotting_thesis/gid/gid_ORandSNP_results.R @@ -76,7 +76,7 @@ foo2 = foo[foo$ligand_distance<10,] table(foo2$ligand_outcome) ############################# -# wide plots SNP +# wide plots SAV # DRUG length(aa_pos_drug); aa_pos_drug drug = foo[foo$position%in%aa_pos_drug,] diff --git a/scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R b/scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R index 50001a5..6508349 100644 --- a/scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R +++ b/scripts/plotting/plotting_thesis/katg/basic_barplots_katg.R @@ -68,7 +68,7 @@ mLigP = stability_count_bp(plotdf = df3_lig , df_colname = "ligand_outcome" #, leg_title = "mCSM-lig" #, bp_plot_title = paste(common_bp_title, "ligand") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nLig" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -116,7 +116,7 @@ if (tolower(gene)%in%geneL_ppi2){ #, label_categories = labels_ppi2 #, bp_plot_title = paste(common_bp_title, "PP-interface") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nPPI2" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -141,7 +141,7 @@ if (tolower(gene)%in%geneL_na){ #, label_categories = #, bp_plot_title = paste(common_bp_title, "Dist to NA") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nNA" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -165,7 +165,7 @@ common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol) posC_lig = site_snp_count_bp(plotdf = df3_lig , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -183,7 +183,7 @@ posC_lig if (tolower(gene)%in%geneL_ppi2){ posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -202,7 +202,7 @@ if (tolower(gene)%in%geneL_ppi2){ if (tolower(gene)%in%geneL_na){ posC_nca = site_snp_count_bp(plotdf = df3_na , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -220,7 +220,7 @@ if (tolower(gene)%in%geneL_na){ #------------------------------ posC_all = site_snp_count_bp(plotdf = df3 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "All mutations sites" @@ -235,7 +235,7 @@ consurfP = stability_count_bp(plotdf = df3 , df_colname = "consurf_outcome" #, leg_title = "ConSurf" #, label_categories = labels_consurf - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "top" , subtitle_text = "ConSurf" , bar_fill_values = consurf_colours # from globals @@ -264,7 +264,7 @@ duetP = stability_count_bp(plotdf = df3 , df_colname = "duet_outcome" , leg_title = "mCSM-DUET" #, label_categories = labels_duet - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-DUET" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -333,7 +333,7 @@ proveanP = stability_count_bp(plotdf = df3 , df_colname = "provean_outcome" #, leg_title = "PROVEAN" #, label_categories = labels_provean - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" # top , subtitle_text = "PROVEAN" , bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep diff --git a/scripts/plotting/plotting_thesis/katg/katg_ORandSNP_results.R b/scripts/plotting/plotting_thesis/katg/katg_ORandSNP_results.R index 4716963..e563807 100644 --- a/scripts/plotting/plotting_thesis/katg/katg_ORandSNP_results.R +++ b/scripts/plotting/plotting_thesis/katg/katg_ORandSNP_results.R @@ -78,7 +78,7 @@ foo2 = foo[foo$ligand_distance<10,] table(foo2$ligand_outcome) ############################# -# wide plots SNP +# wide plots SAV # DRUG length(aa_pos_drug); aa_pos_drug drug = foo[foo$position%in%aa_pos_drug,] diff --git a/scripts/plotting/plotting_thesis/lineage_bp_dist.R b/scripts/plotting/plotting_thesis/lineage_bp_dist.R index d863e8f..9a1a451 100644 --- a/scripts/plotting/plotting_thesis/lineage_bp_dist.R +++ b/scripts/plotting/plotting_thesis/lineage_bp_dist.R @@ -41,7 +41,7 @@ my_yals = 8 # y axis label size my_lls = 8 # legend label size d_lab_size = 2.3 #=============================== -# lineage sample and SNP count +# lineage sample and SAV count #=============================== lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']] , all_lineages = F @@ -58,7 +58,7 @@ lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']] , my_xals = my_xals # x axis label size , my_yals = my_yals # y axis label size , my_lls = my_lls # legend label size - , bar_col_labels = c("nsSNPs", "Total Samples") + , bar_col_labels = c("SAVs", "Total Samples") , bar_col_values = c("grey50", "gray75") , bar_leg_name = "" , leg_location = "top" @@ -68,7 +68,7 @@ lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']] ) lin_countP #=============================== -# lineage SNP diversity count +# lineage SAV diversity count #=============================== lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']] , x_categ = "sel_lineages" @@ -87,8 +87,8 @@ lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']] , y_log10 = F , y_scale_percent = F , leg_location = "top" - , y_label = "Percent" #"SNP diversity" - , bp_plot_title = "nsSNP diversity" + , y_label = "Percent" #"SAV diversity" + , bp_plot_title = "SAV diversity" , title_colour = "black" #"chocolate4" , subtitle_text = NULL , sts = 10 diff --git a/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca.R b/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca.R index d8dd304..01dda2c 100644 --- a/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca.R +++ b/scripts/plotting/plotting_thesis/pnca/basic_barplots_pnca.R @@ -68,7 +68,7 @@ mLigP = stability_count_bp(plotdf = df3_lig , df_colname = "ligand_outcome" #, leg_title = "mCSM-lig" #, bp_plot_title = paste(common_bp_title, "ligand") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nLig" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -116,7 +116,7 @@ if (tolower(gene)%in%geneL_ppi2){ #, label_categories = labels_ppi2 #, bp_plot_title = paste(common_bp_title, "PP-interface") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nPPI2" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -141,7 +141,7 @@ if (tolower(gene)%in%geneL_na){ #, label_categories = #, bp_plot_title = paste(common_bp_title, "Dist to NA") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nNA" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -165,7 +165,7 @@ common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol) posC_lig = site_snp_count_bp(plotdf = df3_lig , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -183,7 +183,7 @@ posC_lig if (tolower(gene)%in%geneL_ppi2){ posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -202,7 +202,7 @@ if (tolower(gene)%in%geneL_ppi2){ if (tolower(gene)%in%geneL_na){ posC_nca = site_snp_count_bp(plotdf = df3_na , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -220,7 +220,7 @@ if (tolower(gene)%in%geneL_na){ #------------------------------ posC_all = site_snp_count_bp(plotdf = df3 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "All mutations sites" @@ -238,7 +238,7 @@ consurfP = stability_count_bp(plotdf = df3 , df_colname = "consurf_outcome" #, leg_title = "ConSurf" #, label_categories = labels_consurf - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "top" , subtitle_text = "ConSurf" , bar_fill_values = consurf_colours_no_isd # from globals @@ -267,7 +267,7 @@ duetP = stability_count_bp(plotdf = df3 , df_colname = "duet_outcome" , leg_title = "mCSM-DUET" #, label_categories = labels_duet - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-DUET" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -336,7 +336,7 @@ proveanP = stability_count_bp(plotdf = df3 , df_colname = "provean_outcome" #, leg_title = "PROVEAN" #, label_categories = labels_provean - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" # top , subtitle_text = "PROVEAN" , bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep diff --git a/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist.R b/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist.R index d863e8f..9a1a451 100644 --- a/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist.R +++ b/scripts/plotting/plotting_thesis/pnca/lineage_bp_dist.R @@ -41,7 +41,7 @@ my_yals = 8 # y axis label size my_lls = 8 # legend label size d_lab_size = 2.3 #=============================== -# lineage sample and SNP count +# lineage sample and SAV count #=============================== lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']] , all_lineages = F @@ -58,7 +58,7 @@ lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']] , my_xals = my_xals # x axis label size , my_yals = my_yals # y axis label size , my_lls = my_lls # legend label size - , bar_col_labels = c("nsSNPs", "Total Samples") + , bar_col_labels = c("SAVs", "Total Samples") , bar_col_values = c("grey50", "gray75") , bar_leg_name = "" , leg_location = "top" @@ -68,7 +68,7 @@ lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']] ) lin_countP #=============================== -# lineage SNP diversity count +# lineage SAV diversity count #=============================== lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']] , x_categ = "sel_lineages" @@ -87,8 +87,8 @@ lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']] , y_log10 = F , y_scale_percent = F , leg_location = "top" - , y_label = "Percent" #"SNP diversity" - , bp_plot_title = "nsSNP diversity" + , y_label = "Percent" #"SAV diversity" + , bp_plot_title = "SAV diversity" , title_colour = "black" #"chocolate4" , subtitle_text = NULL , sts = 10 diff --git a/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob.R b/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob.R index b7aafab..1f3d61e 100644 --- a/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob.R +++ b/scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob.R @@ -68,7 +68,7 @@ mLigP = stability_count_bp(plotdf = df3_lig , df_colname = "ligand_outcome" #, leg_title = "mCSM-lig" #, bp_plot_title = paste(common_bp_title, "ligand") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nLig" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -116,7 +116,7 @@ if (tolower(gene)%in%geneL_ppi2){ #, label_categories = labels_ppi2 #, bp_plot_title = paste(common_bp_title, "PP-interface") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nPPI2" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -141,7 +141,7 @@ if (tolower(gene)%in%geneL_na){ #, label_categories = #, bp_plot_title = paste(common_bp_title, "Dist to NA") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM\nNA" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -165,7 +165,7 @@ common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol) posC_lig = site_snp_count_bp(plotdf = df3_lig , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -183,7 +183,7 @@ posC_lig if (tolower(gene)%in%geneL_ppi2){ posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -202,7 +202,7 @@ if (tolower(gene)%in%geneL_ppi2){ if (tolower(gene)%in%geneL_na){ posC_nca = site_snp_count_bp(plotdf = df3_na , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -220,7 +220,7 @@ if (tolower(gene)%in%geneL_na){ #------------------------------ posC_all = site_snp_count_bp(plotdf = df3 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "All mutations sites" @@ -235,7 +235,7 @@ consurfP = stability_count_bp(plotdf = df3 , df_colname = "consurf_outcome" #, leg_title = "ConSurf" #, label_categories = labels_consurf - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "top" , subtitle_text = "ConSurf" , bar_fill_values = consurf_colours # from globals @@ -264,7 +264,7 @@ duetP = stability_count_bp(plotdf = df3 , df_colname = "duet_outcome" , leg_title = "mCSM-DUET" #, label_categories = labels_duet - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-DUET" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -333,7 +333,7 @@ proveanP = stability_count_bp(plotdf = df3 , df_colname = "provean_outcome" #, leg_title = "PROVEAN" #, label_categories = labels_provean - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" # top , subtitle_text = "PROVEAN" , bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep diff --git a/scripts/plotting/plotting_thesis/rpob/rpob_ORandSNP_results.R b/scripts/plotting/plotting_thesis/rpob/rpob_ORandSNP_results.R index d440193..8a717c1 100644 --- a/scripts/plotting/plotting_thesis/rpob/rpob_ORandSNP_results.R +++ b/scripts/plotting/plotting_thesis/rpob/rpob_ORandSNP_results.R @@ -79,7 +79,7 @@ foo2 = foo[foo$ligand_distance<10,] table(foo2$ligand_outcome) ############################# -# wide plots SNP +# wide plots SAV # DRUG length(aa_pos_drug); aa_pos_drug drug = foo[foo$position%in%aa_pos_drug,] diff --git a/scripts/plotting/plotting_thesis/version1/basic_barplots.R b/scripts/plotting/plotting_thesis/version1/basic_barplots.R index 10f1dc4..a395c59 100644 --- a/scripts/plotting/plotting_thesis/version1/basic_barplots.R +++ b/scripts/plotting/plotting_thesis/version1/basic_barplots.R @@ -11,7 +11,7 @@ # , lts = 20 # legend text size # , ltis = 22 # label title size # , geom_ls = 10 # geom_label size -# , yaxis_title = "Number of nsSNPs" +# , yaxis_title = "Number of SAVs" # , bp_plot_title = "" # , label_categories = c("Destabilising", "Stabilising") # , title_colour = "chocolate4" @@ -94,7 +94,7 @@ mLigP = stability_count_bp(plotdf = df3_lig , df_colname = "ligand_outcome" #, leg_title = "mCSM-lig" #, bp_plot_title = paste(common_bp_title, "ligand") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-lig" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -141,7 +141,7 @@ if (tolower(gene)%in%geneL_ppi2){ #, label_categories = labels_ppi2 #, bp_plot_title = paste(common_bp_title, "PP-interface") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-ppi2" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -167,7 +167,7 @@ if (tolower(gene)%in%geneL_na){ #, label_categories = #, bp_plot_title = paste(common_bp_title, "Dist to NA") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-NA" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -191,7 +191,7 @@ common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol) posC_lig = site_snp_count_bp(plotdf = df3_lig , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -210,7 +210,7 @@ if (tolower(gene)%in%geneL_ppi2){ posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -230,7 +230,7 @@ if (tolower(gene)%in%geneL_na){ posC_nca = site_snp_count_bp(plotdf = df3_na , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -248,7 +248,7 @@ if (tolower(gene)%in%geneL_na){ #------------------------------ posC_all = site_snp_count_bp(plotdf = df3 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "All mutations sites" @@ -263,7 +263,7 @@ consurfP = stability_count_bp(plotdf = df3 , df_colname = "consurf_outcome" #, leg_title = "ConSurf" #, label_categories = labels_consurf - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "top" , subtitle_text = "ConSurf" , bar_fill_values = consurf_colours # from globals @@ -286,7 +286,7 @@ duetP = stability_count_bp(plotdf = df3 , df_colname = "duet_outcome" , leg_title = "mCSM-DUET" #, label_categories = labels_duet - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-DUET" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -359,7 +359,7 @@ proveanP = stability_count_bp(plotdf = df3 , df_colname = "provean_outcome" #, leg_title = "PROVEAN" #, label_categories = labels_provean - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" # top , subtitle_text = "PROVEAN" , bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep diff --git a/scripts/plotting/plotting_thesis/version1/basic_barplots_UPDATED.R b/scripts/plotting/plotting_thesis/version1/basic_barplots_UPDATED.R index 96572e0..89936b9 100644 --- a/scripts/plotting/plotting_thesis/version1/basic_barplots_UPDATED.R +++ b/scripts/plotting/plotting_thesis/version1/basic_barplots_UPDATED.R @@ -60,7 +60,7 @@ mLigP = stability_count_bp(plotdf = df3_lig , df_colname = "ligand_outcome" #, leg_title = "mCSM-lig" #, bp_plot_title = paste(common_bp_title, "ligand") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-lig" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -107,7 +107,7 @@ if (tolower(gene)%in%geneL_ppi2){ #, label_categories = labels_ppi2 #, bp_plot_title = paste(common_bp_title, "PP-interface") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-ppi2" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -133,7 +133,7 @@ if (tolower(gene)%in%geneL_na){ #, label_categories = #, bp_plot_title = paste(common_bp_title, "Dist to NA") - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-NA" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -157,7 +157,7 @@ common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol) posC_lig = site_snp_count_bp(plotdf = df3_lig , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -176,7 +176,7 @@ if (tolower(gene)%in%geneL_ppi2){ posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -196,7 +196,7 @@ if (tolower(gene)%in%geneL_na){ posC_nca = site_snp_count_bp(plotdf = df3_na , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "" @@ -214,7 +214,7 @@ if (tolower(gene)%in%geneL_na){ #------------------------------ posC_all = site_snp_count_bp(plotdf = df3 , df_colname = "position" - , xaxis_title = "Number of nsSNPs" + , xaxis_title = "Number of SAVs" , yaxis_title = "Number of Sites" , subtitle_colour = "chocolate4" , subtitle_text = "All mutations sites" @@ -229,7 +229,7 @@ consurfP = stability_count_bp(plotdf = df3 , df_colname = "consurf_outcome" #, leg_title = "ConSurf" #, label_categories = labels_consurf - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "top" , subtitle_text = "ConSurf" , bar_fill_values = consurf_colours # from globals @@ -252,7 +252,7 @@ duetP = stability_count_bp(plotdf = df3 , df_colname = "duet_outcome" , leg_title = "mCSM-DUET" #, label_categories = labels_duet - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" , subtitle_text = "mCSM-DUET" , bar_fill_values = c("#F8766D", "#00BFC4") @@ -325,7 +325,7 @@ proveanP = stability_count_bp(plotdf = df3 , df_colname = "provean_outcome" #, leg_title = "PROVEAN" #, label_categories = labels_provean - , yaxis_title = "Number of nsSNPs" + , yaxis_title = "Number of SAVs" , leg_position = "none" # top , subtitle_text = "PROVEAN" , bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep diff --git a/scripts/plotting/plotting_thesis/version1/preformatting.R b/scripts/plotting/plotting_thesis/version1/preformatting.R index 127c441..21adddc 100644 --- a/scripts/plotting/plotting_thesis/version1/preformatting.R +++ b/scripts/plotting/plotting_thesis/version1/preformatting.R @@ -85,7 +85,7 @@ foo2 = foo[foo$ligand_distance<10,] table(foo2$ligand_outcome) ############################# -# wide plots SNP +# wide plots SAV # DRUG length(aa_pos_drug); aa_pos_drug drug = foo[foo$position%in%aa_pos_drug,]