DSCAM graphs 2 (normalised)

Splicing In DSCAM

Results - NORMALISED INSTEAD OF LOG

= read/sum(reads) Dataset can be seen [here] https://github.com/OneEsk19/DSCAM/blob/main/norm_reads.csv

# Required libraries
library(ggplot2)
library(gridExtra)

# Load in the data from previous analysis.
dscamSJs <- read.csv(file="dscam_sjs.csv")

# Create a useful subset and rename columns to be easier to work with.
graf <- dscamSJs[,c(3,4,8,11,12)]
id <- 1:63
graf <- cbind(graf, id)
colnames(graf) <- c("start", "end", "reads","Experiment", "Novel", "ID")
sumofreads <- sum(graf$reads)
norm_reads <- graf$reads/sumofreads
graf2 <- cbind(graf, norm_reads)

write.csv(graf2, file = "norm_reads.csv")

ggplot(graf2, aes(x=ID, y=norm_reads)) +
  geom_point(aes(colour = Experiment, shape = Novel), size = 3)+
    scale_shape_manual(values = c(16, 17)) +
  ggtitle("Read Depth of All Splice Junctions")+
  theme(plot.title = element_text(hjust = 0.5))

write.csv(graf2, file="norms.csv")

indb <- graf2[c(16:63), ]
nov <- graf2[c(1:15), ]

g1 <- ggplot(indb, aes(x=ID, y=norm_reads)) +
  geom_point(aes(colour = Experiment), size = 3)+
  ggtitle("Read Depth of Known Splice Junctions(log scale)")+
  theme(plot.title = element_text(hjust = 0.5))
g2 <- ggplot(nov, aes(x=ID, y=norm_reads)) +
  geom_point(aes(colour = Experiment), size = 3)+
  ggtitle("Read Depth of Novel Splice Junctions")+
  theme(plot.title = element_text(hjust = 0.5))
grid.arrange(g1, g2, ncol=1)

With lines instead:

g1 <- ggplot(indb, aes(x=ID, y=norm_reads)) +
  geom_line(aes(colour = Experiment))+
  ggtitle("Read Depth of Known Splice Junctions(log scale)")+
  theme(plot.title = element_text(hjust = 0.5))
g2 <- ggplot(nov, aes(x=ID, y=norm_reads)) +
  geom_line(aes(colour = Experiment))+
  ggtitle("Read Depth of Novel Splice Junctions")+
  theme(plot.title = element_text(hjust = 0.5))
grid.arrange(g1, g2, ncol=1)

Preceeding pipeline: Finding novel splice junctions in RNA-seq data from D. melanogaster DSCAM gene

Log scale graphs