From 375cdc2068619c00bcdcdebcb8c1767d7ef6e6bb Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Thu, 17 Sep 2020 14:01:04 +0100 Subject: [PATCH] added new layput for dm_om and facet_lineage plot --- .../plotting/lineage_dist_dm_om_combined_PS.R | 112 ++++++++++++++---- 1 file changed, 90 insertions(+), 22 deletions(-) diff --git a/scripts/plotting/lineage_dist_dm_om_combined_PS.R b/scripts/plotting/lineage_dist_dm_om_combined_PS.R index 6aa883e..42950c6 100644 --- a/scripts/plotting/lineage_dist_dm_om_combined_PS.R +++ b/scripts/plotting/lineage_dist_dm_om_combined_PS.R @@ -146,6 +146,7 @@ check = u2[!u2%in%u]; print(check) # lineage: labels # from "plyr" #================== +#{Result:No of samples in selected lineages} table(df_lin$lineage) df_lin$lineage_labels = mapvalues(df_lin$lineage @@ -166,6 +167,19 @@ table(df_lin$mutation_info_labels) table(df_lin$mutation_info) == table(df_lin$mutation_info_labels) + +#======================== +# duet_outcome: labels +#======================== +#{Result: No. of D and S mutations in selected lineages} +table(df_lin$duet_outcome) + +df_lin$duet_outcome_labels = ifelse(df_lin$duet_outcome == "Destabilising", "D", "S") +table(df_lin$duet_outcome_labels) + +table(df_lin$duet_outcome) == table(df_lin$duet_outcome_labels) + + #======================= # subset dr muts only #======================= @@ -208,28 +222,37 @@ my_palette <- colorRampPalette(c(mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcs # 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) +# y = duet_outcome +# fill = duet_scaled +# Facet: Lineage #======================================= # 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) +#plot_lineage_dist_duet_f paste0(plotdir,"/", "lineage_dist_duet_f.svg") +#plot_lineage_dist_duet_f +#svg(plot_lineage_dist_duet_f) p1 = ggplot(df, aes(x = duet_scaled - , y = lineage_labels))+ + , y = duet_outcome))+ 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 = my_palette, name = "DUET") + + scale_fill_gradientn(colours = my_palette + , name = "DUET" + #, breaks = c(-1, 0, 1) + #, labels = c(-1,0,1) + #, limits = c(-1,1) + ) + theme(axis.text.x = element_text(size = my_ats , angle = 90 , hjust = 1 , vjust = 0.4) - + #, axis.text.y = element_blank() , axis.text.y = element_text(size = my_ats) , axis.title.x = element_text(size = my_ats) , axis.title.y = element_blank() @@ -237,18 +260,19 @@ p1 = ggplot(df, aes(x = duet_scaled , plot.title = element_blank() , strip.text = 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", )+ + #, legend.title = element_text(size = my_als-6) + , legend.title = element_blank() + , legend.position = c(-0.08, 0.41) + #, legend.direction = "horizontal" + #, legend.position = "left" +)+ labs(x = "DUET") 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))) -#p1_copy +#p1_with_legend = p1 + guides(fill = guide_colourbar(label = FALSE)) + #======================================= # Plot 2: lineage dist: geom_density_ridges, allows alpha to be set # x = duet_scaled @@ -279,14 +303,55 @@ p2 = ggplot(df, aes(x = duet_scaled , axis.ticks.y = element_blank() , plot.title = element_blank() , strip.text = element_text(size = my_als) - , legend.text = element_text(size = my_als-2) - , legend.title = element_text(size = my_als-3) + , legend.text = element_text(size = my_als-4) + , legend.title = element_text(size = my_als-4) , legend.position = c(0.8, 0.9)) + labs(x = "DUET" , fill = "Mutation class") # legend title p2 +#======================================= +# 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 = 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) + +p3 = ggplot(df, aes(x = duet_scaled + , y = lineage_labels))+ + geom_density_ridges_gradient(aes(fill = ..x..) + #, jittered_points = TRUE + , scale = 3 + , size = 0.3 ) + + 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_text(size = my_ats) + , 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-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") + +p3 + ######################################################################## #============== # combine plots @@ -307,11 +372,14 @@ plot_lineage_dist_combined_dm_om_L svg(plot_lineage_dist_combined_dm_om_L, width = 12, height = 6) OutPlot2 = cowplot::plot_grid(p1, p2 - , labels = c("(a)", "(b)") - , rel_widths = c(0.5/2, 0.5/2) - , label_size = my_als) + , labels = c("(a)", "(b)") + #, label_x = -0.045, label_y = 0.92 + #, hjust = -0.7, vjust = -0.5 + #, align = "h" + , rel_widths = c(0.5/2, 0.5/2) + , label_size = my_als) print(OutPlot2) dev.off() -############################################################################## \ No newline at end of file +##############################################################################