diff --git a/scripts/plotting/scratch_plots/lineage_dist_combined_PS_style.R b/scripts/plotting/scratch_plots/lineage_dist_dm_om_combined_PS.R similarity index 74% rename from scripts/plotting/scratch_plots/lineage_dist_combined_PS_style.R rename to scripts/plotting/scratch_plots/lineage_dist_dm_om_combined_PS.R index 89fd5ba..37e8cbe 100644 --- a/scripts/plotting/scratch_plots/lineage_dist_combined_PS_style.R +++ b/scripts/plotting/scratch_plots/lineage_dist_dm_om_combined_PS.R @@ -179,14 +179,9 @@ table(my_df_other$lineage) ######################################################################## #========================== -# Plot 1: ALL Muts -# x = mcsm_values, y = dist -# fill = stability +# Distribution plots #============================ -#my_plot_name_dm_om = 'lineage_dist_DM_OM_PS.svg' -#plot_lineage_dm_om_duet = paste0(plotdir,"/", my_plot_name_dm_om) - #%%%%%%%%%%%%%%%%%%%%%%%%% # REASSIGNMENT df <- df_lin @@ -200,73 +195,29 @@ rm(df_lin) # 2 : ggridges (good!) my_ats = 15 # axis text size my_als = 20 # axis label size - -#======================= -# Plot 1: lineage dist -#======================= -# check plot name -plot_lineage_duet - n_colours = length(unique(df$duet_scaled)) - -#my_palette <- colorRampPalette(c(mcsm_red, "#f8766d", "white","#00bfc4", mcsm_blue))(n = 400) my_palette <- colorRampPalette(c(mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2))(n = n_colours+1) -# output svg -#svg(plot_lineage_duet) +#======================================= +# Plot 1: lineage dist: geom_density_ridges_gradient (allows aesthetics to vary along ridgeline, no alpha setting!) +# else same as geom_density_ridges) +# x = duet_scaled +# y = lineage_labels +# fill = duet_scaled +# NO FACET (nf) +#======================================= +# output individual svg +#plot_lineage_dist_duet_nf = paste0(plotdir,"/", "lineage_dist_duet_nf.svg") +#plot_lineage_dist_duet_nf +#svg(plot_lineage_dist_duet_nf) + p1 = ggplot(df, aes(x = duet_scaled - , y = duet_outcome))+ + , y = lineage_labels))+ geom_density_ridges_gradient(aes(fill = ..x..) #, jittered_points = TRUE , scale = 3 , size = 0.3 ) + - facet_wrap( ~lineage_labels - , scales = "free" - #, labeller = labeller(lineage = my_labels) - ) + coord_cartesian( xlim = c(-1, 1)) + - #scale_fill_gradientn(colours = c("#f8766d", "white", "#00bfc4") - # , name = "DUET" ) + - #scale_fill_gradientn(colours = c(mcsm_red, "#f8766d", "white","#00bfc4", mcsm_blue) - # , name = "DUET" ) + - scale_fill_gradientn(colours = my_palette, name = "DUET") + - theme(axis.text.x = element_text(size = my_ats - , angle = 90 - , hjust = 1 - , vjust = 0.4) - - , axis.text.y = element_blank() - , axis.title.x = element_blank() - , axis.title.y = element_blank() - , axis.ticks.y = element_blank() - , plot.title = element_blank() - , strip.text = element_text(size = my_als) - , legend.text = element_text(size = my_als-6) - , legend.title = element_text(size = my_als-3) - ) - -print(p1) -#dev.off() -#======================================= -# Plot 2: lineage dist by mutation_info -#======================================= - -p2 = ggplot(df, aes(x = duet_scaled - , y = mutation_info_labels))+ - geom_density_ridges_gradient(aes(fill = ..x..) - #, jittered_points = TRUE - , scale = 3 - , size = 0.3 ) + - facet_wrap(~lineage_labels - #, scales = "free" - #, labeller = labeller(lineage = my_labels) - ) + - - coord_cartesian( xlim = c(-1, 1)) + - #scale_fill_gradientn(colours = c("#ae301e", "white", "#007d85") - # , name = "DUET" ) + - #scale_fill_gradientn(colours = c("mcsm_red", "white", "mcsm_blue") - # , name = "DUET" ) + scale_fill_gradientn(colours = my_palette, name = "DUET") + theme(axis.text.x = element_text(size = my_ats , angle = 90 @@ -274,26 +225,42 @@ p2 = ggplot(df, aes(x = duet_scaled , vjust = 0.4) , axis.text.y = element_text(size = my_ats) - , axis.title.x = element_blank() + , axis.title.x = element_text(size = my_ats) , axis.title.y = element_blank() , axis.ticks.y = element_blank() , plot.title = element_blank() , strip.text = element_text(size = my_als) - , legend.position = "none" - #, legend.text = element_text(size = my_als-5) - #, legend.title = element_text(size = my_als) - ) + , legend.text = element_text(size = my_als-10) + , legend.title = element_text(size = my_als-3) + , legend.position = c(0.8, 0.8)) + + #, legend.direction = "horizontal")+ + #, legend.position = "top", )+ + labs(x = "DUET") -print(p2) +p1 -#============================== +#p1_copy = p1 + guides(fill = guide_colourbar(label = FALSE)) +#p1_copy= p1_copy + guides(size=guide_legend("Source", override.aes=list(shape=15, size = 10))) -p3 = ggplot(df, aes(x = duet_scaled +#p1_copy +#======================================= +# Plot 2: lineage dist: geom_density_ridges, allows alpha to be set +# x = duet_scaled +# y = lineage_labels +# fill = mutation_info +# NO FACET +#======================================= +# output svg +#plot_lineage_dist_duet_dm_om = paste0(plotdir,"/", "lineage_dist_duet_dm_om.svg") +#plot_lineage_dist_duet_dm_om +#svg(plot_lineage_dist_duet_dm_om) + +p2 = ggplot(df, aes(x = duet_scaled , y = lineage_labels))+ - geom_density_ridges_gradient(aes(fill = factor(mutation_info_labels)) - #, jittered_points = TRUE - , scale = 3 - , size = 0.3 ) + + geom_density_ridges(aes(fill = factor(mutation_info_labels)) + , scale = 3 + , size = 0.3 + , alpha = 0.8) + coord_cartesian( xlim = c(-1, 1)) + scale_fill_manual(values = c("#E69F00", "#999999")) + theme(axis.text.x = element_text(size = my_ats @@ -309,23 +276,85 @@ p3 = ggplot(df, aes(x = duet_scaled , legend.text = element_text(size = my_als-2) , legend.title = element_text(size = my_als-3) , legend.position = c(0.8, 0.9)) + - labs(x = "DUET", fill = "Mutation class") + labs(x = "DUET" + , fill = "Mutation class") # legend title -# Modify legend titles -#p + labs(fill = "Dose (mg)") - -p3 +p2 ######################################################################## #============== # combine plot #=============== - +plot_lineage_dist_combined_dm_om svg(plot_lineage_dist_combined_dm_om, width = 12, height = 6) -printFile = cowplot::plot_grid(p1, p3 +printFile = cowplot::plot_grid(p1, p2 , rel_widths = c(0.5/2, 0.5/2) , label_size = my_als+10) print(printFile) dev.off() + + +######################################################################## +# alternate combination +######################################################################## +#======================= +# Plot 3: lineage dist: geom_density_ridges_gradient (allows aesthetics to vary along ridgeline, no alpha setting!) +# else same as geom_density_ridges) +# x = duet_scaled +# y = duet_outcome +# FACET (f) = lineage +#======================= + +# output individual svg +#plot_lineage_dist_duet = paste0(plotdir,"/", "lineage_dist_duet_f.svg") +#plot_lineage_dist_duet +#svg(plot_lineage_dist_duet) + +p3 = ggplot(df, aes(x = duet_scaled + , y = duet_outcome))+ + + geom_density_ridges_gradient(aes(fill = ..x..) + , scale = 3 + , size = 0.3) + + + facet_wrap( ~lineage_labels + , scales = "free" + #, labeller = labeller(lineage = my_labels) # sorted by lineage_labels + ) + + coord_cartesian( xlim = c(-1, 1)) + + scale_fill_gradientn(colours = my_palette, name = "DUET") + + theme(axis.text.x = element_text(size = my_ats + , angle = 90 + , hjust = 1 + , vjust = 0.4) + + , axis.text.y = element_blank() + , axis.title.x = element_text(size = my_ats) + , axis.title.y = element_blank() + , axis.ticks.y = element_blank() + , plot.title = element_blank() + , strip.text = element_text(size = my_als) + , legend.text = element_text(size = my_als-6) + , legend.title = element_text(size = my_als-3))+ + labs(x = "DUET") + +print(p3) +#dev.off() + +#============== +# combine plot: alt version +#=============== +plot_lineage_dist_duet_fandnf = paste0(plotdir,"/", "lineage_dist_duet_fandnf.svg") +plot_lineage_dist_duet_fandnf +svg(plot_lineage_dist_duet_fandnf, width = 12, height = 6) + +printFile = cowplot::plot_grid(p3, p2 + , rel_widths = c(0.5/2, 0.5/2) + , label_size = my_als+10) + +print(printFile) +dev.off() + +