library(MASS)
library(RColorBrewer)
rf <- colorRampPalette(rev(brewer.pal(11,'Spectral')))
r <- rf(32)

png("dens_m0_ko_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
a=all_m0[(!is.na(all_m0[,32])&!is.na(all_m0[,16])),]
k2 <- kde2d(log2(1+(a[,32])),log2(1+(a[,16])),n=500,lims=c(0,9,0,9))
#k2=k
#k2$z=log10(k$z+1e-3)
image(k2, col=r,xlab="log2(RPKM_abundance)",ylab="log2(RPKM_translation)")
#contour(k2, add = TRUE,labcex=1)     # from base graphics package
contour(k2, add = TRUE,vfont = c("sans serif", "plain"),labcex=0.65)
dev.off()

png("dens_m0_wt_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
a=all_m0[(!is.na(all_m0[,33])&!is.na(all_m0[,17])),]
k2 <- kde2d(log2(1+(a[,33])),log2(1+(a[,17])),n=500,lims=c(0,9,0,9))
#k2=k
#k2$z=log10(k$z+1e-3)
image(k2, col=r,xlab="log2(RPKM_abundance)",ylab="log2(RPKM_translation)")
#contour(k2, add = TRUE,labcex=1)
contour(k2, add = TRUE,vfont = c("sans serif", "plain"),labcex=0.65)
dev.off()

png("dens_m2_ko_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
a=all_m2[(!is.na(all_m2[,32])&!is.na(all_m2[,16])),]
k2 <- kde2d(log2(1+(a[,32])),log2(1+(a[,16])),n=500,lims=c(0,9,0,9))
#k2=k
#k2$z=log10(k$z+1e-3)
image(k2, col=r,xlab="log2(RPKM_abundance)",ylab="log2(RPKM_translation)")
#contour(k2, add = TRUE,labcex=1)
contour(k2, add = TRUE,vfont = c("sans serif", "plain"),labcex=0.65)
dev.off()

png("dens_m2_wt_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
a=all_m2[(!is.na(all_m2[,33])&!is.na(all_m2[,17])),]
k2 <- kde2d(log2(1+(a[,33])),log2(1+(a[,17])),n=500,lims=c(0,9,0,9))
#k2=k
#k2$z=log10(k$z+1e-3)
image(k2, col=r,xlab="log2(RPKM_abundance)",ylab="log2(RPKM_translation)")
#contour(k2, add = TRUE,labcex=1)
contour(k2, add = TRUE,vfont = c("sans serif", "plain"),labcex=0.65)
dev.off()




#@ diff of log2RPKM
png("dens_m0_diff_ko_minus_wt_rna_vs_poly.png",width=2001,height=2001,pointsize = 44)
a=all_m0[(!is.na(all_m0[,32])&!is.na(all_m0[,16]))&(!is.na(all_m0[,33])&!is.na(all_m0[,17])),]
k <- kde2d(log2(1+(a[,32]))-log2(1+(a[,33])),log2(1+(a[,16]))-log2(1+(a[,17])),n=400,lims=c(-7.4,5.5,-6.1,7.5))
k2=k
k2$z=log10(k$z+1e-12)
image(k2, col=r,xlab="log2 foldchange abundance",ylab="log2 foldchange translation")
grid()
contour(k2, add = TRUE,vfont = c("sans serif", "plain"),labcex=0.65,nlevels=8)     # from base graphics package
dev.off()

png("dens_m1_diff_ko_minus_wt_rna_vs_poly.png",width=2001,height=2001,pointsize = 44)
a=all_m1[(!is.na(all_m1[,32])&!is.na(all_m1[,16]))&(!is.na(all_m1[,33])&!is.na(all_m1[,17])),]
k <- kde2d(log2(1+(a[,32]))-log2(1+(a[,33])),log2(1+(a[,16]))-log2(1+(a[,17])),n=400,lims=c(-7.4,5.5,-6.1,7.5))
k2=k
k2$z=log10(k$z+1e-12)
image(k2, col=r,xlab="log2 foldchange abundance",ylab="log2 foldchange translation")
grid()
contour(k2, add = TRUE,vfont = c("sans serif", "plain"),labcex=0.65,nlevels=8)     # from base graphics package
dev.off()

png("dens_m2_diff_ko_minus_wt_rna_vs_poly.png",width=2001,height=2001,pointsize = 44)
a=all_m2[(!is.na(all_m2[,32])&!is.na(all_m2[,16]))&(!is.na(all_m2[,33])&!is.na(all_m2[,17])),]
k <- kde2d(log2(1+(a[,32]))-log2(1+(a[,33])),log2(1+(a[,16]))-log2(1+(a[,17])),n=400,lims=c(-7.4,5.5,-6.1,7.5))
k2=k
k2$z=log10(k$z+1e-12)
image(k2, col=r,xlab="log2 foldchange abundance",ylab="log2 foldchange translation")
grid()
contour(k2, add = TRUE,vfont = c("sans serif", "plain"),labcex=0.65,nlevels=8)     # from base graphics package
dev.off()

png("dens_2h_diff_ko_minus_wt_rna_vs_poly.png",width=2001,height=2001,pointsize = 44)
a=all_2h[(!is.na(all_2h[,32])&!is.na(all_2h[,16]))&(!is.na(all_2h[,33])&!is.na(all_2h[,17])),]
k <- kde2d(log2(1+(a[,32]))-log2(1+(a[,33])),log2(1+(a[,16]))-log2(1+(a[,17])),n=400,lims=c(-7.4,5.5,-6.1,7.5))
k2=k
k2$z=log10(k$z+1e-12)
image(k2, col=r,xlab="log2 foldchange abundance",ylab="log2 foldchange translation")
grid()
contour(k2, add = TRUE,vfont = c("sans serif", "plain"),labcex=0.65,nlevels=8)     # from base graphics package
dev.off()

png("dens_6h_diff_ko_minus_wt_rna_vs_poly.png",width=2001,height=2001,pointsize = 44)
a=all_6h[(!is.na(all_6h[,32])&!is.na(all_6h[,16]))&(!is.na(all_6h[,33])&!is.na(all_6h[,17])),]
k <- kde2d(log2(1+(a[,32]))-log2(1+(a[,33])),log2(1+(a[,16]))-log2(1+(a[,17])),n=400,lims=c(-7.4,5.5,-6.1,7.5))
k2=k
k2$z=log10(k$z+1e-12)
image(k2, col=r,xlab="log2 foldchange abundance",ylab="log2 foldchange translation")
grid()
contour(k2, add = TRUE,vfont = c("sans serif", "plain"),labcex=0.65,nlevels=8)     # from base graphics package
dev.off()





# test tested genes
a=all_m2[all_m2$geneID.x=="Dab2",]
print(c(log2(1+(a[,32]))-log2(1+(a[,33])),log2(1+(a[,16]))-log2(1+(a[,17]))))

m2:
EnsemblID logFC.x logCPM.x PValue.x FDR.x geneID.x genelength.x CPM_KO_m2_replicate_I.x CPM_KO_m2_replicate_II.x CPM_WT_m2_replicate_I.x CPM_WT_m2_replicate_II.x RPKM_KO_m2_replicate_I.x RPKM_KO_m2_replicate_II.x RPKM_WT_m2_replicate_I.x RPKM_WT_m2_replicate_II.x RPKM_KO_m2.x RPKM_WT_m2.x logFC.y logCPM.y PValue.y FDR.y geneID.y genelength.y CPM_KO_m2_replicate_I.y CPM_KO_m2_replicate_II.y CPM_WT_m2_replicate_I.y CPM_WT_m2_replicate_II.y RPKM_KO_m2_replicate_I.y RPKM_KO_m2_replicate_II.y RPKM_WT_m2_replicate_I.y RPKM_WT_m2_replicate_II.y RPKM_KO_m2.y RPKM_WT_m2.y
ENSMUSG00000022150 0.132107113100571 10.2892120441771 0.331913609425355 1 Dab2 2776.27 1221.56603540568 1395.42241055113 1221.66278736551 1166.31910126626 440.002606160669 502.624892590104 440.037455782582 420.102908314486 471.313749375386 430.070182048534 -1.18653374049147 9.28065118430811 0.00230156674087398 0.0943898662949966 Dab2 2776.27 426.972318667644 326.359251217271 961.026080556944 755.079232071391 153.793513839664 117.553138281677 346.157283173807 271.976152201115 135.67332606067 309.066717687461
ENSMUSG00000033335 -0.0899381293206148 7.71702709380325 0.475478796826375 1 Dnm2 3457.67 208.128905491291 199.505628534437 224.044798713337 209.784286884035 60.1933977190684 57.6994416860017 64.7964666128743 60.6721540470997 58.9464197025351 62.734310329987 -1.84820693331423 5.48337709162363 0.00020140449743313 0.0182692729839096 Dnm2 3457.67 15.3097644143777 20.2567811100375 66.7182064788425 60.3169800767087 4.42776910878646 5.85850619348795 19.2957125691123 17.4444004421211 5.1431376511372 18.3700565056167

m0:
ENSMUSG00000022150 0.384608924394437 8.4667260849825 0.298172975084381 1 Dab2 2776.27 583.223964840449 218.01762162491 255.594292367758 358.125933418394 210.074655865766 78.5289693095087 92.0639175468372 128.995354709158 144.301812587637 110.529636127998 0.516268242555404 7.12196903296183 0.246829592763874 0.775845449687528 Dab2 2776.27 130.920280694042 185.84433363292 107.18913732916 114.792892264839 47.1568978139886 66.9402953001401 38.6090464288991 41.347884847237 57.0485965570644 39.9784656380681
ENSMUSG00000033335 -0.0822073356400329 8.0492193257839 0.707547885501214 1 Dnm2 3457.67 243.646277248694 270.935855038506 270.288103436926 274.478280237585 70.4654513729459 78.3579274593892 78.1705898587563 79.3824396884564 74.4116894161675 78.7765147736063 -0.857910094142138 6.10757625834405 0.0599751124251922 0.442863846034911 Dnm2 3457.67 44.1855947342392 50.0350129011708 83.369329033791 88.3022248191066 12.7790086197466 14.4707311285261 24.1114186818843 25.5380718284587 13.6248698741363 24.8247452551715

Dab2
logFC_rna   =0.132107113100571
log2(136.67332606067)-log2( 310.066717687461)
log2FC_poly= -1.181847
log2FC_rna_m0=0.384608924394437,   log2FC_poly_m0=0.516268242555404
log2FC_rna_m2=0.132107113100571,   log2FC_poly_m2=-1.181847

Dnm2
logFC_rna   = -0.0899381293206148
log2FC_poly= -1.84820693331423
log2FC_rna_m2=-0.0899381293206148, log2FC_poly_m2=-1.84820693331423
-0.0822073356400329 -0.857910094142138