wt=cbind(log2(1+(all_m0[,33])),log2(1+(all_m0[,17])))
ko=cbind(log2(1+(all_m0[,32])),log2(1+(all_m0[,16])))

#wiss={};  for (i in 2:20){k=kmeans(wt, centers=i, iter.max=200);wiss=c(wiss,k$tot.withinss);print(c(i, k$tot.withinss)) }
#plot(wiss)
#opt
i=25;
k=kmeans(wt, centers=i, iter.max=200);
pdf("m0_wt_rna_vs_poly2.pdf")
plot (wt[,1],wt[,2])
points(k$centers, col="red", pch="*")
dev.off()
i=25;
k2=kmeans(ko, centers=i, iter.max=200);
pdf("m0_ko_rna_vs_poly2.pdf")
plot (ko[,1],ko[,2])
points(k2$centers, col="red", pch="*")
dev.off()

#all2_m0=all_m0[(log2(1+all_m0[,17])<1)&(log2(1+all_m0[,16])<1),]
#ks.test(log2(1+(all2_m0[,33])),log2(1+(all2_m0[,32])))




wt=cbind(log2(1+(all_m1[,33])),log2(1+(all_m1[,17])))
ko=cbind(log2(1+(all_m1[,32])),log2(1+(all_m1[,16])))
k=kmeans(wt, centers=i, iter.max=200);
pdf("m1_wt_rna_vs_poly2.pdf")
plot (wt[,1],wt[,2])
points(k$centers, col="red", pch="*")
dev.off()
i=25;
k2=kmeans(ko, centers=i, iter.max=200);
pdf("m1_ko_rna_vs_poly2.pdf")
plot (ko[,1],ko[,2])
points(k2$centers, col="red", pch="*")
dev.off()

wt=cbind(log2(1+(all_m2[,33])),log2(1+(all_m2[,17])))
ko=cbind(log2(1+(all_m2[,32])),log2(1+(all_m2[,16])))
k=kmeans(wt, centers=i, iter.max=200);
pdf("m2_wt_rna_vs_poly2.pdf")
plot (wt[,1],wt[,2])
points(k$centers, col="red", pch="*")
dev.off()
i=25;
k2=kmeans(ko, centers=i, iter.max=200);
pdf("m2_ko_rna_vs_poly2.pdf")
plot (ko[,1],ko[,2])
points(k2$centers, col="red", pch="*")
dev.off()

wt=cbind(log2(1+(all_2h[,33])),log2(1+(all_2h[,17])))
ko=cbind(log2(1+(all_2h[,32])),log2(1+(all_2h[,16])))
k=kmeans(wt, centers=i, iter.max=200);
pdf("2h_wt_rna_vs_poly2.pdf")
plot (wt[,1],wt[,2])
points(k$centers, col="red", pch="*")
dev.off()
i=25;
k2=kmeans(ko, centers=i, iter.max=200);
pdf("2h_ko_rna_vs_poly2.pdf")
plot (ko[,1],ko[,2])
points(k2$centers, col="red", pch="*")
dev.off()

wt=cbind(log2(1+(all_6h[,33])),log2(1+(all_6h[,17])))
ko=cbind(log2(1+(all_6h[,32])),log2(1+(all_6h[,16])))
k=kmeans(wt, centers=i, iter.max=200);
pdf("6h_wt_rna_vs_poly2.pdf")
plot (wt[,1],wt[,2])
points(k$centers, col="red", pch="*")
dev.off()
i=25;
k2=kmeans(ko, centers=i, iter.max=200);
pdf("6h_ko_rna_vs_poly2.pdf")
plot (ko[,1],ko[,2])
points(k2$centers, col="red", pch="*")
dev.off()


require(hexbin)
hbin=hexbin(log2(1+(all_m0[,33])),log2(1+(all_m0[,17])))
pdf("dens_m0_wt_rna_vs_poly.pdf")
plot(hbin)
dev.off()
hbin=hexbin(log2(1+(all_m0[,32])),log2(1+(all_m0[,16])))
pdf("dens_m0_ko_rna_vs_poly.pdf")
plot(hbin)
dev.off()

hbin=hexbin(log2(1+(all_6h[,33])),log2(1+(all_6h[,17])))
pdf("dens_m0_wt_rna_vs_poly.pdf")
plot(hbin)
dev.off()
hbin=hexbin(log2(1+(all_6h[,32])),log2(1+(all_6h[,16])))
pdf("dens_m0_ko_rna_vs_poly.pdf")
plot(hbin)
dev.off()