Nothing
plot_LOGICOIL <-
function(prob.oligo, id)
{
png(sprintf(filename="%s_LOGICOIL.png", id), height=800, width=1200, bg="white", res=300)
par(mar=c(3.5,3.5,0.75,0.75),family="Arial", font=1, cex.lab=0.75, cex.axis=0.75)
mymax <- max(as.numeric(prob.oligo)-1) + 0.1
pal=c("#304E67","darkgreen","tomato","blue")
plot(as.numeric(prob.oligo[,1])-1,
type="h",
col=pal[1],
ylim=c(-mymax, mymax),
lwd=1.5,bty="l",
axes=FALSE,
ann=FALSE,
cex=1.0,
tck=1
)
lines(as.numeric(prob.oligo[,2])-1, type="h", col=pal[2], lwd=1.5)
lines(as.numeric(prob.oligo[,3])-1, type="h", col=pal[4], lwd=1.5)
lines(as.numeric(prob.oligo[,4])-1, type="h", col=pal[3], lwd=1.5)
xlimit <- c()
xlimit <- ceiling(nrow(prob.oligo)/5)*5
axis(1, lwd.ticks=0, at=seq(0,xlimit,5), labels=seq(0,xlimit,5))
axis(2, lwd=0, las=1, at=seq(-1,1,0.25), yaxp=c(0,100,4))
for(y in seq(-1,1,0.25))
{
lines(rep(y, nrow(prob.oligo)), type="s", col="lightgray", lwd=1)
}
mtext("Sequence id",side=1,line=2.5,cex=0.5)
mtext("LOGICOIL scores",side=2,line=2.5,cex=0.5)
legend("topright",ncol=2, c("Antiparallel Dimer","Parallel Dimer","Trimer","Higher-order"), cex=0.5,
col=pal,
lty=1:1, # solid
lwd=2, # line width
bty="n"
)
dev.off()
}
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