Add r-bolero v1.1, new graphics.

src/.docker_modules/r-bolero/1.1/Dockerfile

@@ -12,7 +12,7 @@ RUN apt-get update \
 		libxml2-dev \
 		libharfbuzz-dev \
 		libfribidi-dev \
-		libfreetype6-dev \
+		libfreetype-dev \
 		libpng-dev \
 		libtiff5-dev \
 		libjpeg-dev \

src/.docker_modules/r-bolero/1.1/HBV_RNAs_count.R

@@ -13,7 +13,7 @@ conflict_prefer("filter", "dplyr")
 conflict_prefer("lag", "dplyr")
 
 # source graphical theme:
-source(file="src/ggplot_theme_publication-2.R")
+source("ggplot_theme_Publication-2.R")
 
 # Load files
 option_list = list(
@@ -96,7 +96,11 @@ if (length(countSP$nom) != 0) {
     scale_fill_manual(values = countSP$teinte) +
     labs(fill = "spliced-variants") +
     xlab(element_blank()) + ylab(element_blank()) +
-    scale_colour_Publication() + theme_Publication()
+    scale_colour_Publication() + theme_Publication() +
+    theme(axis.text.y = element_blank(),
+          axis.line.x = element_line(colour=NA),
+          axis.line.y = element_line(colour=NA),
+          axis.ticks = element_blank())
   
   ggsave(file = paste0(opt$barcode, "_SP_proportion_piechart.png"),
          scale = 2,
@@ -233,10 +237,10 @@ ggplot(count_species_clear,
            fill = nom)) +
   geom_col() +
   scale_fill_manual(values = count_species_clear$teinte) +
-  theme(axis.text.x = element_text(angle = 45)) +
-  labs(fill = "RNA species & spliced-variants") +
-  xlab(label = "RNA species & spliced-variants") +
-  scale_colour_Publication() + theme_Publication()
+  labs(fill = element_blank()) +
+  xlab(label = element_blank()) +
+  scale_colour_Publication() + theme_Publication() +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1))
 
 ggsave(file = paste0(opt$barcode, "_count_RNAs_species_clear.png"),
        scale = 2,
@@ -264,8 +268,13 @@ if(nrow(count_clear)!=0){
     geom_col() +
     coord_polar("y") +
     scale_fill_manual(values = count_clear$teinte) +
-    labs(fill = "spliced-variants") +
-    scale_colour_Publication() + theme_Publication()
+    labs(fill = element_blank()) +
+    scale_colour_Publication() + 
+    theme_Publication() +
+    theme(axis.text.y = element_blank(),
+          axis.line.x = element_line(colour=NA),
+          axis.line.y = element_line(colour=NA),
+          axis.ticks = element_blank())
   
   ggsave(file = paste0(opt$barcode, "_SP_clear_proportion_piechart.png"),
          scale = 2,
@@ -279,11 +288,11 @@ ggplot(count_clear, aes(x = nom,
                         fill = nom)) +
   geom_col() +
   scale_fill_manual(values = count_clear$teinte) + 
-  theme(axis.text.x = element_text(angle = 45)) +
-  labs(fill = "spliced-variants") +
-  xlab(label = "spliced-variants") +
+  labs(fill = element_blank()) +
+  xlab(label = element_blank()) +
   ylab(label = "percent") +
-  scale_colour_Publication() + theme_Publication()
+  scale_colour_Publication() + theme_Publication() +
+  theme(axis.text.x = element_text(angle = 45, hjust=1))
 
 ggsave(file = paste0(opt$barcode, "_SP_clear_proportion.png"),
        scale = 2,
@@ -299,10 +308,14 @@ ggplot(count_species_SPxx, aes(x = "species",
   geom_col() +
   coord_polar("y") +
   scale_fill_manual(values = count_species_SPxx$teinte) +
-  labs(fill = "TSS") +
-  ylab(label = "TSS usage") +
-  xlab(label = "percent") +
-  scale_colour_Publication() + theme_Publication()
+  labs(fill = element_blank()) +
+  ylab(label = element_blank()) +
+  xlab(label = element_blank()) +
+  scale_colour_Publication() + theme_Publication() +
+  theme(axis.text.y = element_blank(),
+        axis.line.x = element_line(colour=NA),
+        axis.line.y = element_line(colour=NA),
+        axis.ticks = element_blank())
 
 ggsave(file = paste0(opt$barcode, "_count_RNAs_species_piechart.png"),
        scale = 2,

src/.docker_modules/r-bolero/1.1/Start_positions.R

@@ -17,7 +17,7 @@ conflict_prefer("filter", "dplyr")
 conflict_prefer("lag", "dplyr")
 
 # source graphical theme:
-source(file="src/ggplot_theme_publication-2.R")
+source("ggplot_theme_Publication-2.R")
 
 # Load Start_positions_count files:
 option_list = list(
@@ -68,12 +68,13 @@ df_parsed <- parsingData(sam_bc01)
 ggplot(df_parsed, aes(Start_position, nb_reads)) + 
   geom_area(alpha = 0.5, fill = "blue") + 
   scale_y_sqrt() +
-  facet_wrap(facets = vars(df_parsed$Barcode))
+  facet_wrap(facets = vars(df_parsed$Barcode)) +
   scale_x_continuous(breaks = c(0, 127, 1114, 1490, 2554, 2732, 2907, 3421),
                      label = c("1692", "1819", "2806", "EcoRI", "1065", 
                                "1243", "1418", "1932")) +
   scale_fill_discrete(name="") +
-  scale_colour_Publication() + theme_Publication()+
+  xlab("Position on HBV genome.") + ylab(element_blank()) +
+  scale_colour_Publication() + theme_Publication() +
   theme(axis.text.x = element_text(angle = 45, hjust=1)
   )
 
@@ -201,14 +202,16 @@ plot_camembert <- function(barcode, df, tot) {
                                                        fill=promoters)) +
     geom_col() +
     coord_polar("y") +
-    scale_fill_manual(values = mycolors) +
+    scale_fill_manual(name="", values = mycolors) +
     labs(title = paste0("#reads = ", tot[1,barcode]), 
                         x=element_blank(), 
                         y=element_blank()) +
-    scale_fill_discrete(name="") +
-    scale_colour_Publication() + theme_Publication()+
-    theme(axis.text.x = element_text(angle = 45, hjust=1)
-    )
+    scale_colour_Publication() + theme_Publication() +
+    theme(axis.text.y = element_blank(),
+          axis.line.x = element_line(colour=NA),
+          axis.line.y = element_line(colour=NA),
+          axis.ticks = element_blank())
+    
   
   print(camembert)