library(ballgown)
library(RSkittleBrewer)
library(genefilter)
library(dplyr)
library(devtools)

source("/data/results/tools/rnaseq/ballgown/ballgown/R/myplotTranscripts.R")

samples=c("/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/KO_0h_replicate_I","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/KO_0h_replicate_II","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/KO_2h_replicate_I","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/KO_2h_replicate_II","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/KO_6h_replicate_I","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/KO_6h_replicate_II","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/KO_IFN-gamma_replicate_II","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/KO_IFN_replicate_I","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/KO_IL4_replicate_I","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/KO_IL4_replicate_II","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/WT_0h_replicate_I","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/WT_0h_replicate_II","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/WT_2h_replicate_I","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/WT_2h_replicate_II","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/WT_6h_replicate_I","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/WT_6h_replicate_II","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/WT_IFN-gamma_replicate_I","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/WT_IFN-gamma_replicate_II","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/WT_IL4_replicate_I","/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/ballgown/WT_IL4_replicate_II"	 )

#@ save all:
pheno_data = read.csv("DKphenodata.csv") #pheno_data = read.csv("geuvadis_phenodata.csv")
bg_chrX = ballgown(samples=samples,  pData=pheno_data) #bg_chrX = ballgown(dataDir = "ballgown", samplePattern = "ERR", pData=pheno_data)

#/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/merged.gtf
#chr2	StringTie	transcript	34262291	34299928	1000	+	.	gene_id "MSTRG.11628"; transcript_id "ENSMUST00000149383"; gene_name "Mapkap1"; ref_gene_id "ENSMUSG00000038696"; 
#11628
png("EdgeR Isoform expression in Mapkap1_yellow.png",width=4000,height=2000,pointsize = 22)
myplotTranscripts(ballgown::geneIDs(bg_chrX)[match("MSTRG.11628" ,ballgown::geneIDs(bg_chrX))], bg_chrX,		samples=c("wt01" ,   "wt02" ,   "wt21" ,   "wt22" ,   "wt61" ,   "wt62" ,   "wtIFN1" , "wtIFN2" , "wt01IL4" ,"wt02IL4", "Ko01" ,   "Ko02" ,   "KO21" ,   "KO22" ,   "Ko61" ,   "Ko62" ,   "KOIFN1" , "KOIFN2" , "Ko1IL4" , "Ko2IL4" ),blackBorders=F,labelTranscripts=T)
dev.off()

png("EdgeR Isoform expression in Mapkap1.png",width=4000,height=2000,pointsize = 22)
myplotTranscripts(ballgown::geneIDs(bg_chrX)[match("MSTRG.11628" ,ballgown::geneIDs(bg_chrX))], bg_chrX,		samples=sampleNames(bg_chrX),blackBorders=F,labelTranscripts=T)
dev.off()

png("EdgeR Isoform expression in Mapkap1_with_borders.png",width=4000,height=2000,pointsize = 22)
myplotTranscripts(ballgown::geneIDs(bg_chrX)[match("MSTRG.11628" ,ballgown::geneIDs(bg_chrX))], bg_chrX,		samples=sampleNames(bg_chrX),blackBorders=T,labelTranscripts=T)
dev.off()

png("EdgeR Isoform expression in Mapkap1_2h.png",width=4000,height=2000,pointsize = 22)
myplotTranscripts(ballgown::geneIDs(bg_chrX)[match("MSTRG.11628" ,ballgown::geneIDs(bg_chrX))], bg_chrX,		samples=c("KO_2h_replicate_I","KO_2h_replicate_II","WT_2h_replicate_I","WT_2h_replicate_II"),blackBorders=F,labelTranscripts=T)
dev.off()

png("EdgeR Isoform expression in Mapkap1_2h_with_borders.png",width=4000,height=2000,pointsize = 22)
myplotTranscripts(ballgown::geneIDs(bg_chrX)[match("MSTRG.11628" ,ballgown::geneIDs(bg_chrX))], bg_chrX,		samples=c("KO_2h_replicate_I","KO_2h_replicate_II","WT_2h_replicate_I","WT_2h_replicate_II"),blackBorders=T,labelTranscripts=T)
dev.off()


/data/images/proton/DKlab/orsalia2/stringtie/edgeRtranscriptsExpr-wtVSko.withGID.csv.alt_spliced_in_GE_one_condition.csv
maxAnticorr maxAnticorrCond nAnticorr AvgAnticorr maxAntiIso gene geneName geneID transcriptID "logFC" "logCPM" "PValue" "FDR" "Ko01" "Ko02" "KO21" "KO22" "Ko61" "Ko62" "KOIFN1" "KOIFN2" "Ko1IL4" "Ko2IL4" "wt01" "wt02" "wt21" "wt22" "wt61" "wt62" "wtIFN1" "wtIFN2" "wt01IL4" "wt02IL4" geneName geneID transcriptID "logFC" "logCPM" "PValue" "FDR" "Ko01" "Ko02" "KO21" "KO22" "Ko61" "Ko62" "KOIFN1" "KOIFN2" "Ko1IL4" "Ko2IL4" "wt01" "wt02" "wt21" "wt22" "wt61" "wt62" "wtIFN1" "wtIFN2" "wt01IL4" "wt02IL4"
-0.952056 "Ko01" 15 -0.739618 "ENSMUST00000098950" "Elavl1" NA "MSTRG.14897" "MSTRG.14897.3" -7.40258637479432 5.10482395054949 1.18274679548081e-06 0.00178732288064557 52.2260369328174 60.688312120537 70.0231485299783 65.5926466855231 74.1134992977937 75.5479519811372 88.7418104485808 85.4730298955853 56.4637754093484 54.9474035885586 0 3.67133395277939 0 0.355822223633727 0 0 0 0 0 0 "Elavl1" "MSTRG.14897" "ENSMUST00000098950" 2.31411762421019 4.61977579514688 1.7227373085637e-06 0.00224010252344078 5.17880287296314 4.13635512480044 6.64060587383636 6.90496171131654 10.0291442290727 14.844796230119 12.211909631353 11.6266857341394 4.68369755182191 6.0034993633026 34.6079964049881 22.3564914913987 33.3195225764026 18.324844517137 52.8053582654814 81.763341367952 34.8140672211635 62.2001155276901 22.873502498294 46.0299461174014