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

# Default call 
k <- kde2d(log2(1+(all_m0[,33])),log2(1+(all_m0[,17])))
image(k, col=r)

# Adjust binning (interpolate - can be computationally intensive for large datasets)
k <- kde2d(log2(1+(all_m0[,33])),log2(1+(all_m0[,17])),n=100)
image(k, col=r)
# Contour plot overlayed on heat map image of results
#contour(k, add = TRUE)     # from base graphics package

png("dens_m0_ko_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_m0[,32])),log2(1+(all_m0[,16])),n=200,lims=c(0,13,0,13))
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)     # from base graphics package
dev.off()

png("dens_m0_wt_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_m0[,33])),log2(1+(all_m0[,17])),n=200,lims=c(0,13,0,13))
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)     # from base graphics package
dev.off()

png("dens_m1_ko_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_m1[,32])),log2(1+(all_m1[,16])),n=200,lims=c(0,13,0,13))
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,vfont = c("sans serif", "bold"),labcex=0.65)     # from base graphics package
dev.off()
png("dens_m1_wt_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_m1[,33])),log2(1+(all_m1[,17])),n=200,lims=c(0,13,0,13))
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,vfont = c("sans serif", "bold"),labcex=0.65)     # from base graphics package
dev.off()

png("dens_m2_ko_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_m2[,32])),log2(1+(all_m2[,16])),n=200,lims=c(0,13,0,13))
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,vfont = c("sans serif", "bold"),labcex=0.65)     # from base graphics package
dev.off()
png("dens_m2_wt_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_m2[,33])),log2(1+(all_m2[,17])),n=200,lims=c(0,13,0,13))
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,vfont = c("sans serif", "bold"),labcex=0.65)     # from base graphics package
dev.off()


png("dens_2h_ko_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_2h[,32])),log2(1+(all_2h[,16])),n=200,lims=c(0,13,0,13))
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,vfont = c("sans serif", "bold"),labcex=0.65)     # from base graphics package
dev.off()
png("dens_2h_wt_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_2h[,33])),log2(1+(all_2h[,17])),n=200,lims=c(0,13,0,13))
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,vfont = c("sans serif", "bold"),labcex=0.65)     # from base graphics package
dev.off()

png("dens_6h_ko_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_6h[,32])),log2(1+(all_6h[,16])),n=200,lims=c(0,13,0,13))
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,vfont = c("sans serif", "bold"),labcex=0.65)     # from base graphics package
dev.off()
png("dens_6h_wt_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_6h[,33])),log2(1+(all_6h[,17])),n=200,lims=c(0,13,0,13))
k2=k
k2$z=log10(k$z+1e-3)
image(k2, col=r,xlab="log2(RPKM_abundance)",ylab="log2(RPKM_translation)")
#image(k2, col=r,xlab="log2(RPKM_abundance)",ylab="log2(RPKM_translation)")
contour(k2, add = TRUE,vfont = c("sans serif", "bold"),labcex=0.65)     # from base graphics package
dev.off()




#@ diff of log2RPKM
png("dens_m0_diff_ko_minus_wt_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_m0[,32]))-log2(1+(all_m0[,33])),log2(1+(all_m0[,16]))-log2(1+(all_m0[,17])),n=200,lims=c(-3,3,-2,2))
k2=k
k2$z=log10(k$z+1e-8)
image(k2, col=r,xlab="log2(RPKM_abundance)",ylab="log2(RPKM_translation)")
contour(k2, add = TRUE,vfont = c("sans serif", "plain"),labcex=0.65)     # from base graphics package
dev.off()

png("dens_m1_diff_ko_minus_wt_rna_vs_poly.png",width=1024,height=1024,pointsize = 22)
k <- kde2d(log2(1+(all_m1[,32]))-log2(1+(all_m1[,33])),log2(1+(all_m1[,16]))-log2(1+(all_m1[,17])),n=200,lims=c(-3,3,-2,2))
k2=k
k2$z=log10(k$z+1e-8)
image(k2, col=r,xlab="log2(RPKM_abundance)",ylab="log2(RPKM_translation)")
contour(k2, add = TRUE,vfont = c("sans serif", "plain"),labcex=0.65)     # from base graphics package
dev.off()

#ENSMUSG00000022150 -0.516267828715218 7.12196903296183 0.246853512009843 0.775919770432084 Dab2 2776.27 101.463217537883 130.091033543044 53.5945686645799 79.472002337196 36.5465958058412 46.8582067100981 19.3045232144496 28.6254587403948 41.7024012579696 23.9649909774222

g=all_m0[all_m0$Row.names=="ENSMUSG00000022150",]
print(c(log2(1+(g[,32]))-log2(1+(g[,33])),log2(1+(g[,16]))-log2(1+(g[,17]))))
print(c(log2(1+(g[,32])),log2(1+(g[,16])),log2(1+(g[,33])),log2(1+(g[,17])) ))
5.416245 3.114211 4.641834 2.778624

g=all_m0[all_m0$geneID.x=="Fcgr2b",]
1.651245 5.497498 2.977216 5.716757