Plotting transposons start and end positions

Question

[pinky_pinkpinky]

I have multiple transposons start and end positions in a chromosome.

I want to plot it. I want it without using any bioconductor packages.

Can anyone suggest me how to do?

[Devon Ryan]

Is there a reason why you don't want to use any bioconductor packages?

[pinky_pinkpinky]

I have already plotted in my required scale some other plots without using any packages.

So I felt bit confusing integrating packages with the normal plots.

Answer 1

[Alex Reynolds]

A very rudimentary R script might use plot() and segments():

#!/usr/bin/env Rscript

tpStarts  <- c(5, 10, 20, 25)
tpEnds    <- c(7, 14, 22, 28)
tpYIndex1 <- c(1,  2,  3,  4)
tpYIndex2 <- c(1,  2,  3,  4)
df <- data.frame(tpStarts, tpEnds, tpYIndex1, tpYIndex2)

pdf("graph.pdf", width=5, height=3)
plot(NA, xlim=c(min(df$tpStarts),max(df$tpEnds)), ylim=c(1,4), xlab="Transposon Position", ylab="Transposon Index")
segments(df$tpStarts, df$tpYIndex1, df$tpEnds, df$tpYIndex2, lwd=2)
dev.off()

[pinky_pinkpinky]

Thank you Alex . Is there any other way to get an enlarged view of the positions?

Since the positions looks a bit small in size.

[Alex Reynolds]

You could edit the tpYIndex2 value to be something like c(1.5, 2.5, 3.5, 4.5), etc. also adjusting the ylim maximum to 4.5. You could also edit the lwd parameter upwards to draw thicker lines. Read the R docs on plot() and segments() to see what parameters you can adjust.

[pinky_pinkpinky]

Thank you so much.