#script for the correlation plot grape-MGI

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

####MGI input####
#raw input
d_mel_F_MGI <- read.delim("/users/project/precisiontox_008279/prepilot_3_prime_mgi_03_10_2022/20220912_crosskit_comparision/gene_count_matrix_raw/DF1_DF3_raw_count_mtx_sampleID.tsv",header = TRUE)

rownames(d_mel_F_MGI) <- d_mel_F_MGI$Gene
d_mel_F_MGI <- d_mel_F_MGI[,-1]

tmp <- as.data.frame(str_split_fixed(colnames(d_mel_F_MGI), "\\.", 2))
colnames(d_mel_F_MGI) <- tmp$V1

nms <- unique(names(d_mel_F_MGI))
d_mel_F_MGI <- sapply(nms, function(x)  rowMeans(d_mel_F_MGI[names(d_mel_F_MGI) %in% x]))

####correlation plot####
corr_plot <- ggplot(d_mel_F_MGI,aes(x = log(DF1+1),y = log(DF2+1))) + geom_point(aes(x = log(DF1+1),y = log(DF2+1))) + xlab("log DF1 TPM") + ylab("log DF2 TPM") + sm_corr_theme() + sm_statCorr() + ggtitle("DF1/DF2 MGI correlation")
ggsave(corr_plot,filename = "/users/project/precisiontox_008279/grape-MGI_comaprison/replicate_comparison/grape/results/DF4_DF5_comparison.png")