beeDSCAM

This is based on the tsv file: splice_junction_compared_result_bee.tsv

Is seems like there are a lot more SJs in the bee data!

beeINdb <- beeres[beeres$is_in_gtf_junction == "True",]
dim(beeINdb)

## [1] 28 11

beeNovel <- beeres[beeres$is_in_gtf_junction =="False", ]
dim(beeNovel)

## [1] 1156   11

sumofuniquemapreads <- sum(beeres$number.of.uniquely.mapping.reads.crossing.the.junction)
sumofMMreads <- sum(beeres$number.of.multi.mapping.reads.crossing.the.junction)
beeres$normUreads <- beeres$number.of.uniquely.mapping.reads.crossing.the.junction/sumofuniquemapreads
beeres$normMMreads <- beeres$number.of.multi.mapping.reads.crossing.the.junction/sumofMMreads

beeres$id <- 1:1184
beeConcise <- beeres[, c(14, 11, 2, 3, 10, 7, 12)]
beeConcise$logreads <- log(beeConcise$number.of.uniquely.mapping.reads.crossing.the.junction)
# head(beeConcise)

library(ggplot2)

ggplot(beeConcise, aes(x=id, y=normUreads)) +
  geom_point(aes(colour = Experiment_ID, shape = is_in_gtf_junction), size = 1)+
    scale_shape_manual(values = c(3, 19)) +
  ggtitle("Inclusion Level of All Splice Junctions")+
  theme(plot.title = element_text(hjust = 0.5))

ggplot(beeConcise, aes(x=id, y=logreads)) +
  geom_point(aes(colour = Experiment_ID, shape = is_in_gtf_junction), size = 1)+
    scale_shape_manual(values = c(3 ,19)) +
  ggtitle("logRead Depth of All Splice Junctions")+
  theme(plot.title = element_text(hjust = 0.5))