saving work

scripts/plotting/basic_barplots_LIG.R

@@ -78,7 +78,7 @@ theme_set(theme_grey())
 # start plot 1
 #--------------
 g = ggplot(df, aes(x = ligand_outcome))
-outPlot = g + geom_bar(aes(fill = ligand_outcome)
+OutPlot_lig_count = g + geom_bar(aes(fill = ligand_outcome)
                          , show.legend = TRUE) + 
   geom_label(stat = "count"
              , aes(label = ..count..)
@@ -100,7 +100,7 @@ outPlot = g + geom_bar(aes(fill = ligand_outcome)
   scale_fill_discrete(name = "Ligand Outcome"
                       , labels = c("Destabilising", "Stabilising"))
 
-print(outPlot)
+print(OutPlot_lig_count)
 dev.off()
 
 table(df$ligand_outcome)
@@ -166,7 +166,7 @@ my_als = 22 # axis label size
 my_x = sort(unique(snpsBYpos_df$snpsBYpos)) 
 
 g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
-outPlot_pos = g + geom_bar(aes (alpha = 0.5)
+OutPlot_lig_pos_count = g + geom_bar(aes (alpha = 0.5)
                          , show.legend = FALSE) +
   scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
   #scale_x_continuous(breaks = my_x) +
@@ -185,7 +185,7 @@ outPlot_pos = g + geom_bar(aes (alpha = 0.5)
   labs(x = "Number of SNPs"
        , y = "Number of Sites")
 
-print(outPlot_pos)
+print(OutPlot_lig_pos_count)
 dev.off()
 ########################################################################
 #               			end of lig barplots         			   

scripts/plotting/basic_barplots_PS.R

@@ -64,7 +64,6 @@ str(df)
 # Plot 1:Count of stabilising and destabilsing muts
 #****************
 
-#svg("basic_barplots_PS.svg")
 svg(plot_basic_bp_duet)
 print(paste0("plot1 filename:", basic_bp_duet))
 
@@ -77,7 +76,7 @@ theme_set(theme_grey())
 # start plot 1
 #--------------
 g = ggplot(df, aes(x = duet_outcome))
-outPlot = g + geom_bar(aes(fill = duet_outcome)
+OutPlot_count = g + geom_bar(aes(fill = duet_outcome)
                          , show.legend = TRUE) + 
   geom_label(stat = "count"
              , aes(label = ..count..)
@@ -99,7 +98,7 @@ outPlot = g + geom_bar(aes(fill = duet_outcome)
   scale_fill_discrete(name = "DUET Outcome"
                       , labels = c("Destabilising", "Stabilising"))
 
-print(outPlot)
+print(OutPlot_count)
 dev.off()
 
 table(df$duet_outcome)
@@ -153,7 +152,7 @@ foo = select(df, mutationinformation
 #--------------
 # start plot 2
 #--------------
-#svg("position_count_PS.svg")
+
 svg(plot_pos_count_duet)
 print(paste0("plot filename:", plot_pos_count_duet))
 
@@ -165,7 +164,7 @@ my_als = 22 # axis label size
 my_x = sort(unique(snpsBYpos_df$snpsBYpos)) 
 
 g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
-outPlot_pos = g + geom_bar(aes (alpha = 0.5)
+OutPlot_pos_count = g + geom_bar(aes (alpha = 0.5)
                          , show.legend = FALSE) +
   scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
   #scale_x_continuous(breaks = my_x) +
@@ -184,9 +183,8 @@ outPlot_pos = g + geom_bar(aes (alpha = 0.5)
   labs(x = "Number of SNPs"
        , y = "Number of Sites")
 
-print(outPlot_pos)
+print(OutPlot_pos_count)
 dev.off()
 ########################################################################
 #               			end of Ligand barplots         			   
 ########################################################################
-

scripts/plotting/logo_combined.R

@@ -222,7 +222,8 @@ my_df_snp$log10or = log10(my_df_snp$or_mychisq)
 logo_data = my_df_snp[, c("position", "mutant_type", "or_mychisq", "log10or")]
 
 logo_data_or = my_df_snp[, c("position", "mutant_type", "or_mychisq")]
-wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = 0.0)
+#wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = 0.0)
+wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = NA)
 
 wide_df_or = as.matrix(wide_df_or)
 rownames(wide_df_or) = wide_df_or[,1]

scripts/plotting/other_plots.R

@@ -21,6 +21,10 @@ source("other_plots_data.R")
 dr_other_combined = "dr_other_muts.svg"
 plot_dr_other_combined  =  paste0(plotdir,"/", dr_other_combined)
 
+dr_other_combined_labelled = "dr_other_muts_labelled.svg"
+plot_dr_other_combined_labelled  =  paste0(plotdir,"/", dr_other_combined_labelled)
+
+
 dr_other_foldx = "dr_other_muts_foldx.svg"
 plot_dr_other_foldx  =  paste0(plotdir,"/", dr_other_foldx)
 
@@ -214,6 +218,8 @@ svg(plot_dr_other_combined, width = 24, height = 12)
 
 # first combine fold and lig plots (2 and 3)
 c1 = cowplot::plot_grid(p2, p3
+                        , labels = c("(b)", "(c)")
+                        , label_size = 25
                         , nrow = 1
                         , rel_widths = c(1/6, 5/6))
 c1
@@ -223,6 +229,22 @@ OutPlot = cowplot::plot_grid(p1, c1
 print(OutPlot)
 dev.off()
 
+#==========================================
+# labelled
+cat("Output plot:", plot_dr_other_combined_labelled)
+svg(plot_dr_other_combined_labelled, width = 24, height = 12)
+plot_dr_other_combined_labelled
+
+Outplot_labelled = cowplot::plot_grid(p1, c1
+                        , nrow = 2
+                        , labels = c("(a)", "", "")
+                        , label_size = 25)
+
+print(Outplot_labelled)
+
+dev.off()
+
+
 #---------
 # plot 3: legend
 #---------