diff --git a/src/.docker_modules/r-bolero/1.1/Dockerfile b/src/.docker_modules/r-bolero/1.1/Dockerfile
index dd5a0a3f1fa2386dd32bf84984735d6356478fdd..a9d839790db502bb302b9ac4b773649292719ef5 100644
--- a/src/.docker_modules/r-bolero/1.1/Dockerfile
+++ b/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 \
diff --git a/src/.docker_modules/r-bolero/1.1/HBV_RNAs_count.R b/src/.docker_modules/r-bolero/1.1/HBV_RNAs_count.R
index 6ea15b743b6a9e70a980dde585dbcede3a0bf0aa..e45c1651e44f2236a9b9f9f9c7ee856d9cad8297 100644
--- a/src/.docker_modules/r-bolero/1.1/HBV_RNAs_count.R
+++ b/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$barcode, "_count_RNAs_species_piechart.png"),
scale = 2,
diff --git a/src/.docker_modules/r-bolero/1.1/Start_positions.R b/src/.docker_modules/r-bolero/1.1/Start_positions.R
index 757ffa307c8f9042688e4404ab059fd8efdb0098..e9dbd71377597facf69c9cee65c8e99b4339a850 100644
--- a/src/.docker_modules/r-bolero/1.1/Start_positions.R
+++ b/src/.docker_modules/r-bolero/1.1/Start_positions.R
@@ -17,7 +17,7 @@ conflict_prefer("filter", "dplyr")
conflict_prefer("lag", "dplyr")
# source graphical theme:
-source(file="src/ggplot_theme_publication-2.R")
+source("ggplot_theme_Publication-2.R")
# Load Start_positions_count files:
option_list = list(
@@ -68,12 +68,13 @@ df_parsed <- parsingData(sam_bc01)
ggplot(df_parsed, aes(Start_position, nb_reads)) +
geom_area(alpha = 0.5, fill = "blue") +
scale_y_sqrt() +
- facet_wrap(facets = vars(df_parsed$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)