added new layput for dm_om and facet_lineage plot

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
+# y = duet_outcome
 # fill = duet_scaled
-# NO FACET (nf)
+# Facet: Lineage
 #=======================================
 # output individual svg
-#plot_lineage_dist_duet_nf  =  paste0(plotdir,"/", "lineage_dist_duet_nf.svg")
+#plot_lineage_dist_duet_f  paste0(plotdir,"/", "lineage_dist_duet_f.svg")
-#plot_lineage_dist_duet_nf
+#plot_lineage_dist_duet_f
-#svg(plot_lineage_dist_duet_nf)
+#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.title = element_text(size = my_als-6)
-        , legend.position = c(0.8, 0.8)) +
+        , legend.title = element_blank()
-        #, legend.direction = "horizontal")+
+        , legend.position = c(-0.08, 0.41) 
-        #, legend.position = "top", )+
+        #, 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.text = element_text(size = my_als-4)
-        , legend.title = element_text(size = my_als-3)
+        , 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
@@ -308,6 +373,9 @@ svg(plot_lineage_dist_combined_dm_om_L, width = 12, height = 6)
 
 OutPlot2 = cowplot::plot_grid(p1, p2
                               , 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)