Synodos NF2 kinome baseline data

synodos_nf2_kinome_baseline.R

library(synapser)
synLogin()

library(dplyr)
library(readr)
library(ggplot2)

#Looking at my old analysis scripts (bit messy...sorry), it looks like the baseline kinome data is in a different file, the experiment 
#was probably done before any drug screening had taken place (hence the drug-pertubed kinome analysis was done seperately and later) 
#There's also no syn6. My _guess_ is that this cell line was not tested at the time. Note that Syn1/Syn5 are the isogenic CRISPR pair, 
#Syn6 is also known as Ben-Men-1 and is a well known NF2-/- cell line, but has no isogenic control in the Synodos data
#https://github.com/Sage-Bionetworks/Synodos_NF2/blob/master/kinomeAnalysis/kinomeTranscriptomeIntegration.R

kinome <- synGet('syn6182638')$path %>% 
  readr::read_tsv()


single_kinase_plot <- kinome %>% 
  filter(Gene == "YourKinaseHere",
         cellLine == "Syn5",
         referenceSample == "Syn1") %>%  ##three replicates of each, but analysis was done pairwise to generate 9 different AXL ratios
  ggplot2::ggplot(aes(x = Gene, y = ratio)) +
  geom_boxplot() +
  geom_point()