#script for the correlation plot grape-MGI

####libraries####
packages = c("ggplot2","ggpubr","argparser","smplot")
invisible(lapply(packages, library, character.only = TRUE))
options(bitmapType="cairo")

####input from grape####

##DF4
DF_tmp <- read.delim("/users/project/precisiontox_008279/prepilot_full_length_mgi_15_09_2022/output_all_species/drosophila_melanogaster/work/4a/d0da3e44f0d2886de7b85370f2f5be/DF4-UoB.genes.results")
DF <- DF_tmp[,c(1,6)]
colnames(DF) <- c("gene_id","DF4_TPM")

####DF6
DF_tmp <- read.delim("/users/project/precisiontox_008279/prepilot_full_length_mgi_15_09_2022/output_all_species/drosophila_melanogaster/work/9a/cb507245396f00f5d375d2a1a8f23b/DF6-UoB.genes.results")
DF$DF6_TPM <- DF_tmp[,6]

####DF5
DF_tmp <- read.delim("/users/project/precisiontox_008279/prepilot_full_length_mgi_15_09_2022/output_all_species/drosophila_melanogaster/work/74/d2b531025dc20a2a7ac52dfa9373b5/DF5-UoB.genes.results")
DF$DF5_TPM <- DF_tmp[,6]

####correlation plot####
corr_plot <- ggplot(DF,aes(x = log(DF4_TPM+1),y = log(DF5_TPM+1))) + geom_point(aes(x = log(DF4_TPM+1),y = log(DF5_TPM+1))) + xlab("log DF4 TPM") + ylab("log DF5 TPM") + sm_corr_theme() + sm_statCorr() + ggtitle("DF4/DF5 grape correlation")
ggsave(corr_plot,filename = "/users/project/precisiontox_008279/grape-MGI_comaprison/replicate_comparison/grape/results/DF4_DF5_comparison.png")

corr_plot <- ggplot(DF,aes(x = log(DF4_TPM+1),y = log(DF6_TPM+1))) + geom_point(aes(x = log(DF4_TPM+1),y = log(DF6_TPM+1))) + xlab("log DF4 TPM") + ylab("log DF6 TPM") + sm_corr_theme() + sm_statCorr() + ggtitle("DF4/DF6 grape correlation")
ggsave(corr_plot,filename = "/users/project/precisiontox_008279/grape-MGI_comaprison/replicate_comparison/grape/results/DF4_DF6_comparison.png")