Plotting coverage of annotation over collection of region
If one assumes that repeat elements of a given type (e.g., LINEs) don't overlap each other, then the following will work:


Split your BED file by repeat element, such that you have a LINE.bed, SINE.bed, etc.
Convert those to bedGraph (e.g., awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"1.0"}' LINE.bed &gt; LINE.bedGraph).
Use UCSC tools to convert those bedGraph files to BigWig.
Install deepTools and run computeMatrix reference-point -b 2500 -a 20 -S LINE.bigWig SINE.bigWig LTR.bigWig -R Regions_Of_Interest.BED -o foo.mat.gz
Make a profile plot with plotProfile (plotProfile -m foo.mat.gz -o foo.png --perGroup)


If you do have overlapping regions you'll need to first make a disjoint set of intervals (you can use bedops for this), find the coverage of them (e.g., bedtools coverage) and then continue on with that.