Bee DSCAM: Plots by experiment

Load the data

beeres1 <- read.csv("beedata_tidy.csv")
# head(beeres1)

Produce a more concise table for graphing

beeGrafs <- beeres1[beeres1$number.of.uniquely.mapping.reads.crossing.the.junction != 0,]
beeGrafs$logReads <- log(beeGrafs$number.of.uniquely.mapping.reads.crossing.the.junction)

Splitting by experiment

Exp3962 <- beeGrafs[beeGrafs$Experiment_ID == "3962_1",]
Exp4024 <- beeGrafs[beeGrafs$Experiment_ID == "4024_1",]
EXP4049 <- beeGrafs[beeGrafs$Experiment_ID == "4049_1",]

Add arbitary IDs

Exp3962$id <- 1:476
EXP4049$id <- 1:268
Exp4024$id <- 1:228

Calc inclusion levels for each experiment, may produce nicer graph

e3692sum <- sum(Exp3962$number.of.uniquely.mapping.reads.crossing.the.junction)
Exp3962$IL <- Exp3962$number.of.uniquely.mapping.reads.crossing.the.junction/e3692sum

e4024sum <- sum(Exp4024$number.of.uniquely.mapping.reads.crossing.the.junction)
Exp4024$IL <- Exp4024$number.of.uniquely.mapping.reads.crossing.the.junction/e4024sum

e4049sum <- sum(EXP4049$number.of.uniquely.mapping.reads.crossing.the.junction)
EXP4049$IL <- EXP4049$number.of.uniquely.mapping.reads.crossing.the.junction/e4049sum

library(ggplot2)

## Warning: package 'ggplot2' was built under R version 4.0.3

Plots

Exp 3962

ggplot(Exp3962, aes(x= id, y= logReads)) +
  geom_point(aes(colour = is_in_gtf_junction), size = 2)+
  ggtitle("Log of All Splice Junctions Exp 3962")+
  theme(plot.title = element_text(hjust = 0.5))

ggplot(Exp3962, aes(x= id, y= IL)) +
  geom_point(aes(colour = is_in_gtf_junction), size = 2)+
  ggtitle("Inclusion Level of All Splice Junctions Exp 3962")+
  theme(plot.title = element_text(hjust = 0.5))

______________________________________________________________________________________

Exp4024

ggplot(Exp4024, aes(x= id, y= logReads)) +
  geom_point(aes(colour = is_in_gtf_junction), size = 2)+
  ggtitle("Log of All Splice Junctions Exp4024")+
  theme(plot.title = element_text(hjust = 0.5))

ggplot(Exp4024, aes(x= id, y= IL)) +
  geom_point(aes(colour = is_in_gtf_junction), size = 2)+
  ggtitle("Inclusion Level of All Splice Junctions Exp4024")+
  theme(plot.title = element_text(hjust = 0.5))

______________________________________________________________________________________ EXP4049

ggplot(EXP4049, aes(x= id, y= logReads)) +
  geom_point(aes(colour = is_in_gtf_junction), size = 2)+
  ggtitle("Log of All Splice Junctions EXP4049")+
  theme(plot.title = element_text(hjust = 0.5))

ggplot(EXP4049, aes(x= id, y= IL)) +
  geom_point(aes(colour = is_in_gtf_junction), size = 2)+
  ggtitle("Inclusion Level of All Splice Junctions EXP4049")+
  theme(plot.title = element_text(hjust = 0.5))