cd /data/images/proton/DKlab/orsalia/stringtie
R
require(edgeR)
library(ballgown)
library(RSkittleBrewer)
library(genefilter)
library(dplyr)
library(devtools)
pheno_data = read.csv("DKphenodata.csv") #pheno_data = read.csv("geuvadis_phenodata.csv")
samples=c("./ballgown/Ko01","./ballgown/Ko02","./ballgown/KO21","./ballgown/KO22","./ballgown/Ko61","./ballgown/Ko62","./ballgown/KOIFN1","./ballgown/KOIFN2","./ballgown/Ko1IL4","./ballgown/Ko2IL4","./ballgown/wt01","./ballgown/wt02","./ballgown/wt21","./ballgown/wt22","./ballgown/wt61","./ballgown/wt62","./ballgown/wtIFN1","./ballgown/wtIFN2","./ballgown/wt01IL4","./ballgown/wt02IL4"	 )
#@ save all:
bg_chrX = ballgown(samples=samples,  pData=pheno_data) #bg_chrX = ballgown(dataDir = "ballgown", samplePattern = "ERR", pData=pheno_data)
source("/data/results/tools/rnaseq/ballgown/ballgown/R/myplotTranscripts.R")

/data/images/proton/DKlab/orsalia/stringtie/merged.gtf
chr11	StringTie	transcript	79153195	79158688	1000	+	.	gene_id "MSTRG.2609"; transcript_id "ENSMUST00000145839"; gene_name "Nf1"; ref_gene_id "ENSMUSG00000020716";

myplotTranscripts(ballgown::geneIDs(bg_chrX)[match("MSTRG.2609" ,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)

t_name num_exons length      FPKM.Ko01 FPKM.Ko02 FPKM.KO21 FPKM.KO22 FPKM.Ko61 FPKM.Ko62 FPKM.KOIFN1  FPKM.KOIFN2 FPKM.Ko1IL4 FPKM.Ko2IL4 FPKM.wt01 FPKM.wt02 FPKM.wt21  FPKM.wt22 FPKM.wt61 FPKM.wt62 FPKM.wtIFN1 FPKM.wtIFN2 FPKM.wt01IL4  FPKM.wt02IL4
 ENSMUST00000145839         2    721  0.310171  0.230304  0.474476  0.278064  0.295338  0.337073    0.291509     0.354531    0.098656    0.066897  0.232884  0.237999  0.285587   0.332754  0.371282  0.395558    0.472626    0.390367     0.071044      0.340755
 ENSMUST00000108251        57   9217  1.029450  0.108423  0.024731  0.001685  0.074291  0.057150    0.037325     0.003314    0.009285    0.079847  0.057236  0.062758  1.025612   0.021964  0.013899  0.686524    0.025172    0.041805     0.034540      0.053431
 ENSMUST00000071325        58  11917  1.023349  0.023943  0.014731  0.036099  0.058050  0.036194    0.061642     0.095255    0.010904    0.075958  0.072296  0.140312  1.035741   0.025893  0.080347  1.275790    0.087903    0.048763     0.026794      0.015780
 ENSMUST00000131800        14   3851  0.261503  0.251688  0.321596  0.413339  0.529466  0.248968    0.451557     0.355817    0.225195    0.088342  0.236329  0.354519  0.419832   0.309878  0.574577  0.407341    0.596997    0.284379     0.238720      0.240504
       MSTRG.2609.7        38   5805  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000    0.000000     0.000000    0.000000    0.000000  0.931318  0.000000  0.000000   0.240746  0.255820  0.000000    0.015386    0.000000     0.000000      0.000000
       MSTRG.2609.6        38   5879  0.000000  0.000000  0.000000  0.635300  0.000000  0.091445    0.474742     0.965051    1.212585    0.000000  0.600176  0.000000  0.000000   1.017585  0.314996  0.000000    0.000000    1.150860     0.000000      0.000000
       MSTRG.2609.5        39   5994  0.011156  0.004935  0.005574  1.728529  0.000000  0.087915    1.271910     0.747454    0.700862    0.002654  0.894546  0.000000  0.000000   0.384188  1.310027  0.001181    0.000000    0.617011     0.001219      0.000000
       MSTRG.2609.4        58  11797  0.617656  2.018755  0.075957  0.520783  2.157806  0.085857    1.353197     1.149637    0.876532    0.028880  1.139722  1.935927  0.276369   1.523192  0.705937  0.298342    2.234925    1.664299     1.779060      2.041700
 ENSMUST00000097941        58  11825  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000    0.000000     0.000000    0.000000    0.000000  0.000000  0.000000  0.000000   0.000000  0.000000  0.000000    0.000000    0.000000     0.000000      0.000000
 ENSMUST00000108248        59  11888  0.000000  0.000000  1.761391  0.000000  0.001243  1.541959    0.002231     0.001600    0.000000    1.989305  0.000207  0.000000  0.000000   0.000000  0.000000  0.000000    0.000000    0.000865     0.000000      0.000000
 ENSMUST00000122917        10   1178  0.000000  0.000000  0.183581  0.000000  0.000000  0.159759    0.000000     0.000000    0.000000    0.128951  0.000000  0.000000  0.000000   0.000000  0.000000  0.000000    0.000000    0.000000     0.000000      0.000000
 ENSMUST00000130979         9   1115  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000    0.000000     0.000000    0.000000    0.000000  0.000000  0.000000  0.000000   0.000000  0.000000  0.000000    0.000000    0.000000     0.000000      0.000000
 ENSMUST00000146699        18   4053  0.349606  0.779096  0.894958  1.006292  0.861823  0.538700    0.939775     0.539961    1.168672    0.745545  1.479115  0.555157  0.268275   0.843033  1.076088  0.449389    0.899661    0.991580     0.774226      0.892400
 ENSMUST00000137997        18   4133  0.178095  0.127350  1.973631  2.270687  0.073957  2.235527    0.193456     3.360487    0.275258    0.253382  0.301707  0.160756  0.072764   0.223845  1.956125  0.142361    1.503809    0.112472     0.156075      0.234382

m=read.table("/data/images/proton/DKlab/orsalia/stringtie/nf1-alt-splice-expressions.csv",header=T,sep=" ")
for (i in 0:4){
 exprK=m[,(2*i+1+3)];
 expr=m[,(2*i+1+13)];
 exprK2=m[,(2*i+2+3)];
 expr2=m[,(2*i+2+13)];
 print (colnames(m)[2*i+4])
 dmed=summary(w*(expr+expr2))[3]-summary(w*(exprK+exprK2))[3]
 dmea=summary(w*(expr+expr2))[4]-summary(w*(exprK+exprK2))[4]
print (c(dmed,dmea))

fn=paste("Nf1_TransciptLen_vs_expression_",colnames(m)[2*i+4],".png",sep="");
png(fn,width=1024,height=1024,pointsize = 22)
 plot(l,(expr+expr2),col=cukeCol,main=colnames(m)[2*i+4]);
  points(l,(exprK+exprK2),col=carrotCol,add);
legend('topleft',c('KO','WT'),       fill = c(carrotCol, cukeCol), bty = 'n',       border = NA)
dev.off()
}