how to deal with vector graphics in linux 

you can create pdf files with the R language by using the pdf function:

pdf(file = "norm.pdf", width=20, height=15)


Then use pstoedit to transform the pdf into svg:

pstoedit -f plot-svg rnorm.pdf rnorm.svg

Then this file can be edited with inkscape.

inkscape scatterplot_coverage_edited.svg --export-pdf scatterplot_coverage_edited.pdf

Recent versions of inkscape can directly import pdfs.