diff --git a/scripts/functions/bp_subcolours.R b/scripts/functions/bp_subcolours.R index 2465f0d..f6b384e 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 SAVs" + , my_ylab = "" # Custom 2: x-axis: geom tiles ~ lig distance #, A_xvar_lig = T diff --git a/scripts/functions/position_annotation.R b/scripts/functions/position_annotation.R index 1290f6b..cfb439d 100644 --- a/scripts/functions/position_annotation.R +++ b/scripts/functions/position_annotation.R @@ -13,7 +13,8 @@ position_annotation=function(plot_df, drug_colour='green', lig1_colour='slategrey', lig2_colour='navyblue', - lig3_colour='purple' + lig3_colour='purple', + x_label=NULL ) { x_ats = 12 @@ -107,9 +108,9 @@ position_annotation=function(plot_df, theme(plot.background = element_rect(fill = bg, colour=NA), #plot.margin = margin(t=0,b=0), panel.background = element_rect(fill = bg, colour=NA), - legend.position = "none" + legend.position = "none", axis.title.x = element_text(size = 8) ) + - labs(x = NULL, y= NULL) + + labs(x = x_label, y= NULL) + geom_tile(aes(y = 1,x=reorder(position,-pos_count), fill = bg_all, colour = bg_all) ) + geom_tile(aes(y = 2, x=reorder(position,-pos_count), fill = col_bg1, colour = col_bg1) @@ -146,9 +147,9 @@ position_annotation=function(plot_df, theme(plot.background = element_rect(fill = bg, colour=NA), #plot.margin = margin(t=0,b=0), panel.background = element_rect(fill = bg, colour=NA), - legend.position = "none" + legend.position = "none", axis.title.x = element_text(size = 8) ) + - labs(x = NULL, y= NULL) + + labs(x = x_label, y= NULL) + geom_tile(aes(y = 1, x=factor(position), fill = bg_all, colour = bg_all) ) + geom_tile(aes(y = 2, x=factor(position), fill = col_bg1, colour = col_bg1) diff --git a/scripts/plotting/plotting_thesis/thesis-figs-alr.R b/scripts/plotting/plotting_thesis/thesis-figs-alr.R index ab4afff..be88c57 100644 --- a/scripts/plotting/plotting_thesis/thesis-figs-alr.R +++ b/scripts/plotting/plotting_thesis/thesis-figs-alr.R @@ -166,7 +166,7 @@ print(paste0("Plotting LOW Rows: ", nrow(small_df3))) logo_p_snps_low = LogoPlotSnps( mutable_df3, - y_lab="", + y_lab="SAV Diversity", aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, @@ -195,7 +195,7 @@ logo_or_low = LogoPlotCustomH( lig3_colour = tile_map$tile_colour[4] ) -stability_low = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +stability_low = stab()+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) # MID @@ -205,7 +205,7 @@ print(paste0("Plotting MID Rows: ", nrow(small_df3))) logo_p_snps_centre = LogoPlotSnps( mutable_df3, - y_lab = "", + y_lab = "SAV Diversity", aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, @@ -231,7 +231,7 @@ logo_or_centre = LogoPlotCustomH( lig3_colour = tile_map$tile_colour[4] ) -stability_centre = stab(my_ylab="SAV Count") +stability_centre = stab() # HIGH small_df3 = merged_df3[merged_df3['position'] > centre,] @@ -241,7 +241,7 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3))) logo_p_snps_high = LogoPlotSnps( mutable_df3, - y_lab="" , + y_lab="SAV Diversity" , aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, @@ -251,7 +251,7 @@ logo_p_snps_high = LogoPlotSnps( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) logo_or_high = LogoPlotCustomH( small_df3, @@ -267,10 +267,10 @@ logo_or_high = LogoPlotCustomH( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) -stability_high = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +stability_high = stab()+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) #### "sorted" stability plots #### # do stability plots for later assembly @@ -292,9 +292,10 @@ stability_high_reorder = bp_stability_hmap( drug_colour = tile_map$tile_colour[1], lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] + lig3_colour = tile_map$tile_colour[4], + x_label="Wild-Type Position" -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +) stability_centre_reorder = bp_stability_hmap( snpcount_low_high_df, reorder_position = T, diff --git a/scripts/plotting/plotting_thesis/thesis-figs-embb.R b/scripts/plotting/plotting_thesis/thesis-figs-embb.R index 0c2f5f6..ad0cdd3 100644 --- a/scripts/plotting/plotting_thesis/thesis-figs-embb.R +++ b/scripts/plotting/plotting_thesis/thesis-figs-embb.R @@ -12,6 +12,7 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") #outdir="/home/pub/Work/LSHTM/Thesis_Plots/" outdir="~/git/Writing/thesis/tex/images-corrected/embb/" +#outdir="~/tmp/embb/" # add "pos_count" position count column merged_df3=merged_df3 %>% dplyr::add_count(position) @@ -83,8 +84,9 @@ stability_low = bp_stability_hmap(snpcount_low_low_df, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, aa_pos_lig2=aa_pos_lig2, - aa_pos_lig3=aa_pos_lig3 -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) + aa_pos_lig3=aa_pos_lig3, + x_label="Wild-Type Position" +) low=round(max(merged_df3$position)/3) centre=low*2 @@ -175,7 +177,7 @@ print(paste0("Plotting LOW Rows: ", nrow(small_df3))) logo_p_snps_low = LogoPlotSnps(mutable_df3, - y_lab="", + y_lab="SAV Diversity", aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, @@ -207,13 +209,13 @@ logo_p_snps_centre = LogoPlotSnps( aa_pos_lig1=aa_pos_lig1, aa_pos_lig2=aa_pos_lig2, aa_pos_lig3=aa_pos_lig3, - y_lab = "SAV Count" + y_lab = "SAV Diversity" ) logo_or_centre = LogoPlotCustomH(small_df3, - y_axis_increment=2, - y_lab = "Log(10) Odds Ratio", - y_axis_log = TRUE, + y_axis_increment=10, + y_lab = "Odds Ratio", + y_axis_log = FALSE, rm_empty_y=T, aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, @@ -229,14 +231,14 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3))) logo_p_snps_high = LogoPlotSnps(mutable_df3, - y_lab="", + y_lab="SAV Diversity", x_lab = "Position", aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, aa_pos_lig2=aa_pos_lig2, aa_pos_lig3=aa_pos_lig3 -) + annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +) + annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) logo_or_high = LogoPlotCustomH(small_df3, @@ -248,7 +250,7 @@ logo_or_high = LogoPlotCustomH(small_df3, aa_pos_lig1=aa_pos_lig1, aa_pos_lig2=aa_pos_lig2, aa_pos_lig3=aa_pos_lig3 -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) jpeg(paste0(outdir,"embb_average_stability.jpeg"), height = 8.25, width=11.5, unit="in",res=300) cowplot::plot_grid( diff --git a/scripts/plotting/plotting_thesis/thesis-figs-gid.R b/scripts/plotting/plotting_thesis/thesis-figs-gid.R index 5d587f1..c1f6d94 100644 --- a/scripts/plotting/plotting_thesis/thesis-figs-gid.R +++ b/scripts/plotting/plotting_thesis/thesis-figs-gid.R @@ -136,7 +136,7 @@ stab=function(...){bp_stability_hmap( yvar_colname = 'avg_stability_scaled', stability_colname = "avg_stability_scaled", stability_outcome_colname = "avg_stability_outcome", - my_ylab = "", + #my_ylab = "", my_xaxls = 6, # x-axis label size my_yaxls = 8, # y-axis label size drug_colour = tile_map$tile_colour[1], @@ -163,7 +163,7 @@ print(paste0("Plotting LOW Rows: ", nrow(small_df3))) logo_p_snps_low = LogoPlotSnps( mutable_df3, - y_lab="", + y_lab="SAV Diversity", aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, @@ -203,7 +203,7 @@ mutable_df3 = cbind(small_df3) print(paste0("Plotting MID Rows: ", nrow(small_df3))) logo_p_snps_centre = LogoPlotSnps( mutable_df3, - y_lab = "", + y_lab = "SAV Diversity", aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, @@ -229,7 +229,26 @@ logo_or_centre = LogoPlotCustomH( lig3_colour = tile_map$tile_colour[4] ) -stability_centre = stab() +stability_centre = bp_stability_hmap( + small_df3, + p_title = NULL, + yvar_colname = 'avg_stability_scaled', + stability_colname = "avg_stability_scaled", + stability_outcome_colname = "avg_stability_outcome", + my_ylab = "SAV Count", + my_xaxls = 6, # x-axis label size + my_yaxls = 8, # y-axis label size + drug_colour = tile_map$tile_colour[1], + lig1_colour = tile_map$tile_colour[2], + lig2_colour = tile_map$tile_colour[3], + lig3_colour = tile_map$tile_colour[4], + y_max_override=max(merged_df3$pos_count), + aa_pos_drug=aa_pos_drug, + active_aa_pos=active_aa_pos, + aa_pos_lig1=aa_pos_lig1, + aa_pos_lig2=aa_pos_lig2, + aa_pos_lig3=aa_pos_lig3 +) # HIGH small_df3 = merged_df3[merged_df3['position'] > centre,] @@ -239,7 +258,7 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3))) logo_p_snps_high = LogoPlotSnps( mutable_df3, - y_lab="" , + y_lab="SAV Diversity" , aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, @@ -249,7 +268,7 @@ logo_p_snps_high = LogoPlotSnps( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) logo_or_high = LogoPlotCustomH( small_df3, @@ -265,10 +284,10 @@ logo_or_high = LogoPlotCustomH( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) -stability_high = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +stability_high = stab(x_label="Wild-Type Position") #### "sorted" stability plots #### # do stability plots for later assembly diff --git a/scripts/plotting/plotting_thesis/thesis-figs-katg.R b/scripts/plotting/plotting_thesis/thesis-figs-katg.R index 682fe4a..9b69dd9 100644 --- a/scripts/plotting/plotting_thesis/thesis-figs-katg.R +++ b/scripts/plotting/plotting_thesis/thesis-figs-katg.R @@ -165,7 +165,7 @@ print(paste0("Plotting LOW Rows: ", nrow(small_df3))) logo_p_snps_low = LogoPlotSnps( mutable_df3, - y_lab="", + y_lab="SAV Diversity", aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, @@ -195,7 +195,7 @@ logo_or_low = LogoPlotCustomH( lig3_colour = tile_map$tile_colour[4] ) -stability_low = stab()+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +stability_low = stab(x_label="Wild-Type Position") # MID @@ -205,7 +205,7 @@ print(paste0("Plotting MID Rows: ", nrow(small_df3))) logo_p_snps_centre = LogoPlotSnps( mutable_df3, - y_lab = "", + y_lab = "SAV Diversity", aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, @@ -244,7 +244,7 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3))) logo_p_snps_high = LogoPlotSnps( mutable_df3, - y_lab="" , + y_lab="SAV Diversity" , aa_pos_drug=aa_pos_drug, active_aa_pos=active_aa_pos, aa_pos_lig1=aa_pos_lig1, @@ -254,7 +254,7 @@ logo_p_snps_high = LogoPlotSnps( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) logo_or_high = LogoPlotCustomH( small_df3, @@ -271,7 +271,7 @@ logo_or_high = LogoPlotCustomH( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) stability_high = stab() @@ -298,7 +298,7 @@ stability_high_reorder = bp_stability_hmap( lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) stability_centre_reorder = bp_stability_hmap( snpcount_low_high_df, reorder_position = T, @@ -340,8 +340,9 @@ stability_low_reorder = bp_stability_hmap( drug_colour = tile_map$tile_colour[1], lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] - + lig3_colour = tile_map$tile_colour[4], + x_label="Wild-Type Position" + ) jpeg(paste0(outdir,"katg_average_stability-sorted.jpeg"), height = 6, width=11.5, unit="in",res=300) diff --git a/scripts/plotting/plotting_thesis/thesis-figs-rpob.R b/scripts/plotting/plotting_thesis/thesis-figs-rpob.R index 5857d52..91e5ac6 100644 --- a/scripts/plotting/plotting_thesis/thesis-figs-rpob.R +++ b/scripts/plotting/plotting_thesis/thesis-figs-rpob.R @@ -164,7 +164,7 @@ print(paste0("Plotting LOW Rows: ", nrow(small_df3))) logo_p_snps_low = LogoPlotSnps( mutable_df3, - y_lab="", + y_lab="SAV Diversity", active_aa_pos=active_aa_pos, aa_pos_drug=aa_pos_drug, aa_pos_lig1=aa_pos_lig1, @@ -204,7 +204,7 @@ print(paste0("Plotting MID Rows: ", nrow(small_df3))) logo_p_snps_centre = LogoPlotSnps( mutable_df3, - y_lab = "", + y_lab = "SAV Diversity", x_ats = 4.5, active_aa_pos=active_aa_pos, aa_pos_drug=aa_pos_drug, @@ -246,7 +246,7 @@ print(paste0("Plotting HIGH Rows: ", nrow(small_df3))) logo_p_snps_high = LogoPlotSnps( mutable_df3, - y_lab=" " , + y_lab="SAV Diversity" , x_ats = 5, active_aa_pos=active_aa_pos, aa_pos_drug=aa_pos_drug, @@ -257,7 +257,7 @@ logo_p_snps_high = LogoPlotSnps( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) logo_or_high = LogoPlotCustomH( small_df3, @@ -274,10 +274,11 @@ logo_or_high = LogoPlotCustomH( lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) -stability_low = stab(my_xaxls = 4)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +stability_low = stab(my_xaxls = 4, + x_label="Wild-Type Position") #### "sorted" stability plots #### # do stability plots for later assembly @@ -301,7 +302,7 @@ stability_high_reorder = bp_stability_hmap( lig2_colour = tile_map$tile_colour[3], lig3_colour = tile_map$tile_colour[4] -)+ annotate(geom="text", label="Position",x=0.5,y=0.025, size=3) +)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3) stability_centre_reorder = bp_stability_hmap( snpcount_low_high_df, reorder_position = T, @@ -343,7 +344,8 @@ stability_low_reorder = bp_stability_hmap( drug_colour = tile_map$tile_colour[1], lig1_colour = tile_map$tile_colour[2], lig2_colour = tile_map$tile_colour[3], - lig3_colour = tile_map$tile_colour[4] + lig3_colour = tile_map$tile_colour[4], + x_label="Wild-Type Position" )