require(reshape2)
library(ggplot2)
library(plyr)
library(dplyr)
library(plotly)
library(reshape2)


data <- read.table("RGs data_new.txt",header=T)
rownames(data) <- data[,1]

data<-data[,sort(names(data), decreasing=TRUE)]
str(data)

mylabels <- c(expression(paste(italic("XPO1"))),
              expression(paste(italic("THOC5"))),
              expression(paste(italic("SMARCA5"))),
              expression(paste(italic("OASL"))),
              expression(paste(italic("NADK"))),
              expression(paste(italic("LSM14A"))),
              expression(paste(italic("HNRNPUL1"))), 
              expression(paste(italic("HNRNPR"))), 
              expression(paste(italic("HNRNPL"), " (exon 4)")),
              expression(paste(italic("HNRNPL"))),
              expression(paste(italic("GDI1"))), 
              expression(paste(italic("EMC4"))),
              expression(paste(italic("C26H12orf43"))),
              expression(paste(italic("BAG6"), " (exon 4)")), 
              expression(paste(italic("ANKFY1"))))

xaxislabel <- c(expression(paste(italic("Cq "), "values (adjusted to ", italic("E "), "= 1)")))

ggplot(data = melt(data), aes(y=value, color=variable, x = variable))+
  stat_boxplot(geom ='errorbar', width = 0.25) + 
  geom_boxplot(fill='#FFFFFF',
               outlier.color ='NA',
               outlier.shape=1,
               fatten=2,
               lwd=0.5,
               width=0.4) +
  coord_flip()+ 
  theme_classic()+
  theme(axis.title.x=element_text(size=17),
        axis.title.y=element_blank(),
        axis.text.x = element_text(color="black", size= 14),
        axis.text.y = element_text(color="black", size = 14))+
  scale_x_discrete(labels = mylabels)+
  labs(y= xaxislabel)+
  scale_y_continuous(breaks=seq(19,27,1))+
  
  scale_color_manual(values = c( '#0000b2', '#0000b2', '#0000b2', '#960032', '#0000b2', '#0000b2', '#0000b2', '#0000b2', '#808080', '#0000b2', '#0000b2', '#0000b2','#960032', '#808080', '#0000b2'),
                     breaks = c("ANKFY1", "BAG6_exon4", "C26H12orf43"),
                     labels=c("exon pair", "single exon", "context RG"),
                     name= element_blank())+
  theme(legend.title=element_text(face="bold",size=15))+
  theme(legend.text=element_text(size=13))+
  geom_jitter(width = 0, height = 0, aes(shape= Sample), size=1.5)+
  scale_shape_manual(values=c(8, 0, 1, 2, 6, 3, 4))