RNA+poly for M0,1,2
for
Tf->Trf
Apoe,C3,Calr,Cbl,Dab2,Dnm1,Dnm2,Dock2,Fcgr2b,Nckap1l,Plcg2,Itsn1,Trf,Ankfy1,Camk1d,Ano6
~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq-vs-polysomeseq/rna_poly_m2_pcg.csv
#use macro to make heatmap-degs-mX.txt

#zz=gzfile('/data/images/proton2/run423/wwwDouniLab/metaseqr_run423d/lists/metaseqr_all_out_wt_vs_tg.txt.gz','rt')
require(made4)
x=read.table("~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq-vs-polysomeseq/heatmap-degs-m0.txt",header=T)
m0r1=log2( (1+x$CPM_KO_0h_replicate_I.x)/(1+x$CPM_WT_0h_replicate_I.x) )
m0r2=log2( (1+x$CPM_KO_0h_replicate_II.x)/(1+x$CPM_WT_0h_replicate_II.x) )
m0p1=log2( (1+x$CPM_KO_0h_replicate_I.y)/(1+x$CPM_WT_0h_replicate_I.y) )
m0p2=log2( (1+x$CPM_KO_0h_replicate_II.y)/(1+x$CPM_WT_0h_replicate_II.y) )
x=read.table("~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq-vs-polysomeseq/heatmap-degs-m1.txt",header=T)
m1r1=log2( (1+x$CPM_KO_m1_replicate_I.x)/(1+x$CPM_WT_m1_replicate_I.x) )
m1r2=log2( (1+x$CPM_KO_m1_replicate_II.x)/(1+x$CPM_WT_m1_replicate_II.x) )
m1p1=log2( (1+x$CPM_KO_m1_replicate_I.y)/(1+x$CPM_WT_m1_replicate_I.y) )
m1p2=log2( (1+x$CPM_KO_m1_replicate_II.y)/(1+x$CPM_WT_m1_replicate_II.y) )
x=read.table("~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq-vs-polysomeseq/heatmap-degs-m2.txt",header=T)
m2r1=log2( (1+x$CPM_KO_m2_replicate_I.x)/(1+x$CPM_WT_m2_replicate_I.x) )
m2r2=log2( (1+x$CPM_KO_m2_replicate_II.x)/(1+x$CPM_WT_m2_replicate_II.x) )
m2p1=log2( (1+x$CPM_KO_m2_replicate_I.y)/(1+x$CPM_WT_m2_replicate_I.y) )
m2p2=log2( (1+x$CPM_KO_m2_replicate_II.y)/(1+x$CPM_WT_m2_replicate_II.y) )
cl=cbind(m0r1,m0r2,m1r1,m1r2,m2r1,m2r2,m0p1,m0p2,m1p1,m1p2,m2p1,m2p2)
rownames(cl)=x$geneID.x
colnames(cl)=c("M0_RNA_rep1","M0_RNA_rep2","M1_RNA_rep1","M1_RNA_rep2","M2_RNA_rep1","M2_RNA_rep2","M0_POLY_rep1","M0_POLY_rep2","M1_POLY_rep1","M1_POLY_rep2","M2_POLY_rep1","M2_POLY_rep2")
 
png("M2-TopCateg-DEG-heatmap-ave-dualScale.png",width=1411,height=1501,pointsize = 28)
 heatplot(cl,scale="row", returnSampleTree=TRUE,method="ave",cexRow=1,cexCol=1,srtCol=45,dend="row",dualScale=T,lhei = c(0.25,1),margins=c(7.1,5.1))
dev.off()
png("M2-TopCateg-DEG-heatmap-ave-dualScale-vertLabels.png",width=1411,height=1501,pointsize = 28)
 heatplot(cl,scale="row", returnSampleTree=TRUE,method="ave",cexRow=1,cexCol=1,dend="row",dualScale=T,lhei = c(0.25,1),margins=c(7.5,5.1))
dev.off()

#same with RPKM instead og CPM
x=read.table("~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq-vs-polysomeseq/heatmap-degs-m0.txt",header=T)
m0r1=log2( (1+x$RPKM_KO_0h_replicate_I.x)/(1+x$RPKM_WT_0h_replicate_I.x) )
m0r2=log2( (1+x$RPKM_KO_0h_replicate_II.x)/(1+x$RPKM_WT_0h_replicate_II.x) )
m0p1=log2( (1+x$RPKM_KO_0h_replicate_I.y)/(1+x$RPKM_WT_0h_replicate_I.y) )
m0p2=log2( (1+x$RPKM_KO_0h_replicate_II.y)/(1+x$RPKM_WT_0h_replicate_II.y) )
x=read.table("~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq-vs-polysomeseq/heatmap-degs-m1.txt",header=T)
m1r1=log2( (1+x$RPKM_KO_m1_replicate_I.x)/(1+x$RPKM_WT_m1_replicate_I.x) )
m1r2=log2( (1+x$RPKM_KO_m1_replicate_II.x)/(1+x$RPKM_WT_m1_replicate_II.x) )
m1p1=log2( (1+x$RPKM_KO_m1_replicate_I.y)/(1+x$RPKM_WT_m1_replicate_I.y) )
m1p2=log2( (1+x$RPKM_KO_m1_replicate_II.y)/(1+x$RPKM_WT_m1_replicate_II.y) )
x=read.table("~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq-vs-polysomeseq/heatmap-degs-m2.txt",header=T)
m2r1=log2( (1+x$RPKM_KO_m2_replicate_I.x)/(1+x$RPKM_WT_m2_replicate_I.x) )
m2r2=log2( (1+x$RPKM_KO_m2_replicate_II.x)/(1+x$RPKM_WT_m2_replicate_II.x) )
m2p1=log2( (1+x$RPKM_KO_m2_replicate_I.y)/(1+x$RPKM_WT_m2_replicate_I.y) )
m2p2=log2( (1+x$RPKM_KO_m2_replicate_II.y)/(1+x$RPKM_WT_m2_replicate_II.y) )
cl=cbind(m0r1,m0r2,m1r1,m1r2,m2r1,m2r2,m0p1,m0p2,m1p1,m1p2,m2p1,m2p2)
rownames(cl)=x$geneID.x
colnames(cl)=c("M0_RNA_rep1","M0_RNA_rep2","M1_RNA_rep1","M1_RNA_rep2","M2_RNA_rep1","M2_RNA_rep2","M0_POLY_rep1","M0_POLY_rep2","M1_POLY_rep1","M1_POLY_rep2","M2_POLY_rep1","M2_POLY_rep2")
 
png("M2-TopCateg-DEG-RPKM-heatmap-ave-dualScale.png",width=1411,height=1501,pointsize = 28)
 heatplot(cl,scale="row", returnSampleTree=TRUE,method="ave",cexRow=1,cexCol=1,srtCol=45,dend="row",dualScale=T,lhei = c(0.25,1),margins=c(7.1,5.1))
dev.off()


png("M2-TopCateg-DEG-RPKM-heatmap-ave-dualScale-vertLabels.png",width=1411,height=1501,pointsize = 28)
 heatplot(cl,scale="row", returnSampleTree=TRUE,method="ave",cexRow=1,cexCol=1,dend="row",dualScale=T,lhei = c(0.25,1),margins=c(7.5,5.1))
dev.off()