source("/data/results/tools/rnaseq/ballgown/ballgown/R/myplotTranscripts.R") png("EdgeR Isoform expression in Mapkap1_yellow.png",width=4000,height=2000,pointsize = 22) myplotTranscripts(ballgown::geneIDs(bg_chrX)[match("MSTRG.8671" ,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() "ENSMUST00000149383" "ENSMUST00000124443" "ENSMUST00000141253" "ENSMUST00000156967" "ENSMUST00000113124" "ENSMUST00000113129" "ENSMUST00000113123" "ENSMUST00000040459" "MSTRG.8671.9" "ENSMUST00000147337" "ENSMUST00000113126" "ENSMUST00000138933" "ENSMUST00000137021" "ENSMUST00000129633" 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 49889 0.000000 0.038438 0.023375 0.049442 0.065998 0.045236 0.000000 0.000000 0.072895 0.000000 0.059182 0.000000 0.000000 0.047286 0.022122 0.000000 0.000000 0.000000 0.000000 0.000000 49890 0.291924 0.557944 0.180571 0.455069 0.876211 0.225356 0.334117 0.009553 0.000139 0.934988 0.000235 1.662696 0.082874 0.590783 0.074551 0.158323 0.063429 0.262547 1.079108 0.157984 49891 0.067316 0.048982 0.056100 0.224231 0.161774 0.132328 0.104063 0.016137 0.258586 0.087574 0.171952 0.355450 0.225491 0.487244 0.093958 0.369015 0.102509 0.060580 0.106608 0.089736 49892 0.000000 0.000000 0.066747 0.000000 0.000000 0.043405 0.000000 0.000000 0.053705 0.000000 0.000000 0.028553 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 49893 0.504058 0.000000 0.736178 0.000000 0.000000 0.000000 0.000000 0.000000 0.706336 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 49894 0.164791 1.224742 0.137894 1.025934 0.475445 0.394216 0.987704 0.449901 0.117569 0.950980 0.494854 1.846860 0.101161 0.000000 0.144014 0.062965 0.260690 0.541850 0.640523 0.197267 49895 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 49896 2.617989 9.420318 4.111584 5.545094 3.032947 4.146778 2.223907 5.619954 3.668113 3.656590 8.626937 6.903143 0.924306 3.554783 0.546525 0.407015 0.406623 4.556520 5.596998 0.864372 49897 0.019853 1.842643 0.575802 0.846920 0.605627 1.190231 3.076615 3.422852 5.006593 2.432391 1.871926 0.218022 0.047704 1.782447 0.015334 0.016798 0.000000 0.881993 1.458919 0.028957 49898 6.142202 2.139267 3.140017 2.459947 2.052425 1.249335 1.160212 1.201370 1.907533 2.299499 0.911919 0.384060 0.048375 1.648541 0.011651 0.007192 0.105616 1.491005 1.672212 0.032870 49900 1.647346 2.161907 1.107964 1.119766 1.319876 0.691548 0.623703 0.297878 1.147742 1.584701 1.815260 2.980576 13.256781 0.636997 10.299870 9.660767 8.729104 0.951891 1.192665 13.164365 49902 0.009908 0.000000 0.000000 0.066765 0.000000 0.049452 0.174878 0.037109 0.119466 0.000000 0.161950 0.000000 0.000000 0.000000 0.000000 0.025959 0.000000 0.131310 0.000000 0.000000 49903 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 49905 0.027979 0.029307 0.012041 0.005408 0.046083 0.034025 0.015098 0.016125 0.036794 0.014241 0.039873 0.000000 0.000000 0.008344 0.035268 0.024945 0.017957 0.014312 0.071788 0.029993 49889 49890 49891 "ENSMUST00000149383" "ENSMUST00000124443" "ENSMUST00000141253" 49892 49893 49894 "ENSMUST00000156967" "ENSMUST00000113124" "ENSMUST00000113129" 49895 49896 49897 "ENSMUST00000113123" "ENSMUST00000040459" "MSTRG.8671.9" 49898 49900 49902 "ENSMUST00000147337" "ENSMUST00000113126" "ENSMUST00000138933" 49903 49905 "ENSMUST00000137021" "ENSMUST00000129633" m=read.table("/data/images/proton/DKlab/orsalia/stringtie/mapkap1-alt-splice-expressions.csv",header=T,sep=",") mw=m[,4:23] l=m[,3] for (i in 1:10){ exprK=m[,(i+3)]; expr=m[,(i+13)]; print (colnames(m)[i+3]) dmed=summary(w*expr)[3]-summary(w*exprK)[3] dmea=summary(w*expr)[4]-summary(w*exprK)[4] print (c(dmed,dmea)) # plot(w,expr); } carrotCol <- rgb(1,0,0,0.8) cukeCol <- rgb(0,0,1,0.8) 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("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=T); legend('topleft',c('KO','WT'), fill = c(carrotCol, cukeCol), bty = 'n', border = NA) dev.off() } #@ 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) FPKM.Ko01 FPKM.Ko02 FPKM.KO21 FPKM.KO22 FPKM.Ko61 FPKM.Ko62 FPKM.KOIFN1 15546 0.310171 0.230304 0.474476 0.278064 0.295338 0.337073 0.291509 15547 1.029450 0.108423 0.024731 0.001685 0.074291 0.057150 0.037325 15548 1.023349 0.023943 0.014731 0.036099 0.058050 0.036194 0.061642 15549 0.261503 0.251688 0.321596 0.413339 0.529466 0.248968 0.451557 15550 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15551 0.000000 0.000000 0.000000 0.635300 0.000000 0.091445 0.474742 15552 0.011156 0.004935 0.005574 1.728529 0.000000 0.087915 1.271910 15553 0.617656 2.018755 0.075957 0.520783 2.157806 0.085857 1.353197 15554 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15555 0.000000 0.000000 1.761391 0.000000 0.001243 1.541959 0.002231 15557 0.000000 0.000000 0.183581 0.000000 0.000000 0.159759 0.000000 15558 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15572 0.349606 0.779096 0.894958 1.006292 0.861823 0.538700 0.939775 15573 0.178095 0.127350 1.973631 2.270687 0.073957 2.235527 0.193456 FPKM.KOIFN2 FPKM.Ko1IL4 FPKM.Ko2IL4 FPKM.wt01 FPKM.wt02 FPKM.wt21 15546 0.354531 0.098656 0.066897 0.232884 0.237999 0.285587 15547 0.003314 0.009285 0.079847 0.057236 0.062758 1.025612 15548 0.095255 0.010904 0.075958 0.072296 0.140312 1.035741 15549 0.355817 0.225195 0.088342 0.236329 0.354519 0.419832 15550 0.000000 0.000000 0.000000 0.931318 0.000000 0.000000 15551 0.965051 1.212585 0.000000 0.600176 0.000000 0.000000 15552 0.747454 0.700862 0.002654 0.894546 0.000000 0.000000 15553 1.149637 0.876532 0.028880 1.139722 1.935927 0.276369 15554 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15555 0.001600 0.000000 1.989305 0.000207 0.000000 0.000000 15557 0.000000 0.000000 0.128951 0.000000 0.000000 0.000000 15558 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15572 0.539961 1.168672 0.745545 1.479115 0.555157 0.268275 15573 3.360487 0.275258 0.253382 0.301707 0.160756 0.072764 FPKM.wt22 FPKM.wt61 FPKM.wt62 FPKM.wtIFN1 FPKM.wtIFN2 FPKM.wt01IL4 15546 0.332754 0.371282 0.395558 0.472626 0.390367 0.071044 15547 0.021964 0.013899 0.686524 0.025172 0.041805 0.034540 15548 0.025893 0.080347 1.275790 0.087903 0.048763 0.026794 15549 0.309878 0.574577 0.407341 0.596997 0.284379 0.238720 15550 0.240746 0.255820 0.000000 0.015386 0.000000 0.000000 15551 1.017585 0.314996 0.000000 0.000000 1.150860 0.000000 15552 0.384188 1.310027 0.001181 0.000000 0.617011 0.001219 15553 1.523192 0.705937 0.298342 2.234925 1.664299 1.779060 15554 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15555 0.000000 0.000000 0.000000 0.000000 0.000865 0.000000 15557 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15558 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15572 0.843033 1.076088 0.449389 0.899661 0.991580 0.774226 15573 0.223845 1.956125 0.142361 1.503809 0.112472 0.156075 FPKM.wt02IL4 15546 0.340755 15547 0.053431 15548 0.015780 15549 0.240504 15550 0.000000 15551 0.000000 15552 0.000000 15553 2.041700 15554 0.000000 15555 0.000000 15557 0.000000 15558 0.000000 15572 0.892400 15573 0.234382 t_id chr strand start end t_name num_exons length 15546 15546 chr11 + 79153195 79158688 ENSMUST00000145839 2 721 15547 15547 chr11 + 79153294 79392444 ENSMUST00000108251 57 9217 15548 15548 chr11 + 79153327 79395114 ENSMUST00000071325 58 11917 15549 15549 chr11 + 79153389 79244290 ENSMUST00000131800 14 3851 15550 15550 chr11 + 79153389 79350991 MSTRG.2609.7 38 5805 15551 15551 chr11 + 79153389 79351062 MSTRG.2609.6 38 5879 15552 15552 chr11 + 79153389 79351114 MSTRG.2609.5 39 5994 15553 15553 chr11 + 79153389 79395053 MSTRG.2609.4 58 11797 15554 15554 chr11 + 79153394 79395111 ENSMUST00000097941 58 11825 15555 15555 chr11 + 79153394 79395111 ENSMUST00000108248 59 11888 15557 15557 chr11 + 79261655 79286914 ENSMUST00000122917 10 1178 15558 15558 chr11 + 79261655 79286914 ENSMUST00000130979 9 1115 15572 15572 chr11 + 79350410 79383617 ENSMUST00000146699 18 4053 15573 15573 chr11 + 79359810 79393550 ENSMUST00000137997 18 4133 gene_id gene_name cov.Ko01 FPKM.Ko01 cov.Ko02 FPKM.Ko02 cov.KO21 15546 MSTRG.2609 Nf1 2.470395 0.310171 2.335729 0.230304 4.617496 15547 MSTRG.2609 Nf1 8.199171 1.029450 1.099616 0.108423 0.240676 15548 MSTRG.2609 Nf1 8.150580 1.023349 0.242828 0.023943 0.143362 15549 MSTRG.2609 Nf1 2.082774 0.261503 2.552602 0.251688 3.129703 15550 MSTRG.2609 . 0.000000 0.000000 0.000000 0.000000 0.000000 15551 MSTRG.2609 . 0.000000 0.000000 0.000000 0.000000 0.000000 15552 MSTRG.2609 . 0.088855 0.011156 0.050050 0.004935 0.054244 15553 MSTRG.2609 . 4.919391 0.617656 20.474102 2.018755 0.739198 15554 MSTRG.2609 Nf1 0.000000 0.000000 0.000000 0.000000 0.000000 15555 MSTRG.2609 Nf1 0.000000 0.000000 0.000000 0.000000 17.141462 15557 MSTRG.2609 Nf1 0.000000 0.000000 0.000000 0.000000 1.786566 15558 MSTRG.2609 Nf1 0.000000 0.000000 0.000000 0.000000 0.000000 15572 MSTRG.2609 Nf1 2.784474 0.349606 7.901549 0.779096 8.709535 15573 MSTRG.2609 Nf1 1.418457 0.178095 1.291575 0.127350 19.206944 FPKM.KO21 cov.KO22 FPKM.KO22 cov.Ko61 FPKM.Ko61 cov.Ko62 FPKM.Ko62 15546 0.474476 2.678902 0.278064 2.706136 0.295338 3.655856 0.337073 15547 0.024731 0.016230 0.001685 0.680719 0.074291 0.619839 0.057150 15548 0.014731 0.347786 0.036099 0.531903 0.058050 0.392557 0.036194 15549 0.321596 3.982157 0.413339 4.851415 0.529466 2.700276 0.248968 15550 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15551 0.000000 6.120557 0.635300 0.000000 0.000000 0.991801 0.091445 15552 0.005574 16.652861 1.728529 0.000000 0.000000 0.953515 0.087915 15553 0.075957 5.017286 0.520783 19.771626 2.157806 0.931193 0.085857 15554 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15555 1.761391 0.000000 0.000000 0.011386 0.001243 16.723915 1.541959 15557 0.183581 0.000000 0.000000 0.000000 0.000000 1.732723 0.159759 15558 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15572 0.894958 9.694737 1.006292 7.896749 0.861823 5.842682 0.538700 15573 1.973631 21.876081 2.270687 0.677659 0.073957 24.246273 2.235527 cov.KOIFN1 FPKM.KOIFN1 cov.KOIFN2 FPKM.KOIFN2 cov.Ko1IL4 FPKM.Ko1IL4 15546 2.933032 0.291509 3.095995 0.354531 0.961445 0.098656 15547 0.375551 0.037325 0.028939 0.003314 0.090489 0.009285 15548 0.620211 0.061642 0.831826 0.095255 0.106263 0.010904 15549 4.543355 0.451557 3.107219 0.355817 2.194630 0.225195 15550 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15551 4.776633 0.474742 8.427438 0.965051 11.817190 1.212585 15552 12.797380 1.271910 6.527246 0.747454 6.830218 0.700862 15553 13.615251 1.353197 10.039360 1.149637 8.542200 0.876532 15554 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15555 0.022445 0.002231 0.013969 0.001600 0.000000 0.000000 15557 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15558 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15572 9.455588 0.939775 4.715283 0.539961 11.389244 1.168672 15573 1.946470 0.193456 29.345917 3.360487 2.682514 0.275258 cov.Ko2IL4 FPKM.Ko2IL4 cov.wt01 FPKM.wt01 cov.wt02 FPKM.wt02 cov.wt21 15546 0.671924 0.066897 1.699346 0.232884 1.755404 0.237999 1.962204 15547 0.801994 0.079847 0.417653 0.057236 0.462882 0.062758 7.046747 15548 0.762939 0.075958 0.527543 0.072296 1.034899 0.140312 7.116344 15549 0.887327 0.088342 1.724490 0.236329 2.614820 0.354519 2.884568 15550 0.000000 0.000000 6.795810 0.931318 0.000000 0.000000 0.000000 15551 0.000000 0.000000 4.379474 0.600176 0.000000 0.000000 0.000000 15552 0.026662 0.002654 6.527480 0.894546 0.000000 0.000000 0.000000 15553 0.290075 0.028880 8.316523 1.139722 14.278805 1.935927 1.898870 15554 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15555 19.980942 1.989305 0.001514 0.000207 0.000000 0.000000 0.000000 15557 1.295204 0.128951 0.000000 0.000000 0.000000 0.000000 0.000000 15558 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15572 7.488390 0.745545 10.793071 1.479115 4.094666 0.555157 1.843258 15573 2.545018 0.253382 2.201551 0.301707 1.185683 0.160756 0.499943 FPKM.wt21 cov.wt22 FPKM.wt22 cov.wt61 FPKM.wt61 cov.wt62 FPKM.wt62 15546 0.285587 2.654791 0.332754 2.905111 0.371282 3.016644 0.395558 15547 1.025612 0.175232 0.021964 0.108750 0.013899 5.235641 0.686524 15548 1.035741 0.206580 0.025893 0.628682 0.080347 9.729566 1.275790 15549 0.419832 2.472282 0.309878 4.495803 0.574577 3.106505 0.407341 15550 0.000000 1.920727 0.240746 2.001678 0.255820 0.000000 0.000000 15551 0.000000 8.118526 1.017585 2.464699 0.314996 0.000000 0.000000 15552 0.000000 3.065144 0.384188 10.250364 1.310027 0.009009 0.001181 15553 0.276369 12.152378 1.523192 5.523636 0.705937 2.275247 0.298342 15554 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15555 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15557 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15558 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15572 0.268275 6.725910 0.843033 8.419897 1.076088 3.427181 0.449389 15573 0.072764 1.785884 0.223845 15.305788 1.956125 1.085691 0.142361 cov.wtIFN1 FPKM.wtIFN1 cov.wtIFN2 FPKM.wtIFN2 cov.wt01IL4 FPKM.wt01IL4 15546 3.660146 0.472626 4.033956 0.390367 0.631956 0.071044 15547 0.194941 0.025172 0.432006 0.041805 0.307247 0.034540 15548 0.680745 0.087903 0.503900 0.048763 0.238339 0.026794 15549 4.623308 0.596997 2.938699 0.284379 2.123477 0.238720 15550 0.119154 0.015386 0.000000 0.000000 0.000000 0.000000 15551 0.000000 0.000000 11.892705 1.150860 0.000000 0.000000 15552 0.000000 0.000000 6.376045 0.617011 0.010844 0.001219 15553 17.307873 2.234925 17.198456 1.664299 15.825213 1.779060 15554 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15555 0.000000 0.000000 0.008936 0.000865 0.000000 0.000000 15557 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15558 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 15572 6.967224 0.899661 10.246747 0.991580 6.886947 0.774226 15573 11.645912 1.503809 1.162253 0.112472 1.388326 0.156075 cov.wt02IL4 FPKM.wt02IL4 15546 2.329912 0.340755 15547 0.365336 0.053431 15548 0.107898 0.015780 15549 1.644445 0.240504 15550 0.000000 0.000000 15551 0.000000 0.000000 15552 0.000000 0.000000 15553 13.960142 2.041700 15554 0.000000 0.000000 15555 0.000000 0.000000 15557 0.000000 0.000000 15558 0.000000 0.000000 15572 6.101789 0.892400 15573 1.602588 0.234382 15546 15547 15548 "ENSMUST00000145839" "ENSMUST00000108251" "ENSMUST00000071325" 15549 15550 15551 "ENSMUST00000131800" "MSTRG.2609.7" "MSTRG.2609.6" 15552 15553 15554 "MSTRG.2609.5" "MSTRG.2609.4" "ENSMUST00000097941" 15555 15557 15558 "ENSMUST00000108248" "ENSMUST00000122917" "ENSMUST00000130979" 15572 15573 "ENSMUST00000146699" "ENSMUST00000137997"