Commit c2a5022b authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
Browse files

Modify

parent 6c4b2490
......@@ -313,16 +313,17 @@ heatmap.2(as.matrix(all.hf.mapped[,-c(1:2)]), scale="none", dendrogram="none", l
### Plot MG and MT mapping separately
row.sort <- c("SM", "HF1", "HF2", "HF3", "HF4", "HF5", "WW1", "WW2", "WW3", "WW4", "BG")
#col.sort <- c("IMP", "IMP-megahit", "IMP_MG", "MOCAT_MG", "MetAmos_MG", "IMP_MT", "IGC")
col.sort <- c("IMP", "IMP-megahit", "IMP_MG", "MOCAT_MG", "MetAmos_MG", "IGC")
#col.sort <- c("IMP", "IMP-megahit", "IMP_MG", "MOCAT_MG", "MetAmos_MG", "IGC")
col.sort <- c("IMP", "IMP-megahit", "IMP_MG", "MOCAT_MG", "MetAmos_MG")
#annot.cols <- c(rep("purple", 2), rep("darkblue", 3), "darkred", "black" )
annot.cols <- c(rep("purple", 2), rep("darkblue", 3), "black" )
annot.cols <- c(rep("purple", 2), rep("darkblue", 3))
### Plot MG reads mapping
MG.mapped <- acast(m.dat[m.dat$variable=="MG_properly_paired",-3], Dataset~Assembly)
MG.mapped <- MG.mapped[row.sort,col.sort]
colnames(MG.mapped)[5] <- "MetAMOS_MG"
pdf("/home/shaman/Documents/Publications/IMP-manuscript/figures/second_iteration/MG_mapping-v4.pdf")
pdf("/home/shaman/Documents/Publications/IMP-manuscript/figures/second_iteration/MG_mapping-v5.pdf")
heatmap.2(as.matrix(MG.mapped), scale="row", dendrogram="none",
col=colorRampPalette(c("white", "blue", "darkblue"), space="rgb"), na.color="gray25",
trace="none",
......@@ -335,12 +336,11 @@ heatmap.2(as.matrix(MG.mapped), scale="row", dendrogram="none",
dev.off()
### Plot MT reads mapping
MT.mapped <- acast(m.dat[m.dat$variable=="MT_properly_paired",-3], Dataset~Assembly)
MT.mapped <- MT.mapped[row.sort,col.sort]
colnames(MT.mapped)[5] <- "MetAMOS_MG"
pdf("/home/shaman/Documents/Publications/IMP-manuscript/figures/second_iteration/MT_mapping-v4.pdf")
pdf("/home/shaman/Documents/Publications/IMP-manuscript/figures/second_iteration/MT_mapping-v5.pdf")
heatmap.2(as.matrix(MT.mapped), scale="row", dendrogram="none",
col=colorRampPalette(c("white", "red", "darkred"), space="rgb"), na.color="gray25",
trace="none",
......
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