This article describes feature frequency histograms and how to configure them in GBrowse.
For the main GBrowse configuration article, see: GBrowse Configuration.
Note: this applies to GFF2 databases only and needs to be rewritten slightly for GFF3
With a little bit of additional effort, you can set one or more tracks up to display a density histogram of the features contained within the track. For example, the human data source in the GBrowse demo uses density histograms in the chromosomal overview. In addition, when the features in the SNP track become too dense to view, this track converts into a histogram. To see this in action, turn on the SNP track and then zoom out beyond 150K - Link plz?
There are four steps for making histograms:
bp_generate_histogram.pl
script.bp_load_gff.pl or
bp_fast_load_gff.pl.The first step is to generate the density data. Currently this is done
by generating a GFF file containing a set of “bin” feature types. Use
the bp_generate_histogram.pl script to do this. You will find it in
BioPerl under the scripts/Bio-DB-GFF
directory.
Assuming that your database is named “dicty”, you have a feature named SNP, and you wish to generate a density distribution across 10,000 bp bins, here is the command you would use:
bp_generate_histogram.pl -merge -d dicty -bin 10000 SNP >snp_density.gff
This is saying to use the “dicty” database (-d) option, to use 10,000 bp bins (the -bin option) and to count the occurrences of the SNP feature throughout the database. In addition, the -merge option says to merge all types of SNPs into a single bin. Otherwise they will be stratified by their source. The resulting GFF file contains a series of entries like these ones:
Chr1 SNP bin 1 10000 49 + . bin Chr1:SNP
Chr1 SNP bin 10001 20000 29 + . bin Chr1:SNP
What this is saying is that there are now a series of pseudo-features of type “bin:SNP” that occupy successive 10,000 bp regions of the genome. The score field contains the number of times a SNP was seen in that bin.
You’ll now load this file using bp_load_gff.pl or
bp_fast_load_gff.pl:
bp_load_gff.pl -d dicty snp_density.gff
The next step is to tell GBrowse how to use this information. You do this by creating a new aggregator for the SNP density information. Open the GBrowse configuration file and find the aggregators option. Add a new aggregator that looks like this:
aggregators = snp_density{bin:SNP}
This is declaring a new feature named “snp_density” that is composed of subparts of type bin:SNP.
The last step is to declare a track for the density information. You will use the “xyplot” glyph, which can draw a number of graphs, including histograms. To add the SNP density information as a static track in the overview, create a section like this one:
[SNP:overview]
feature = snp_density
glyph = xyplot
graph_type = boxes
scale = right
bgcolor = red
fgcolor = red
height = 20
key = SNP Density
This article describes glyphs and glyph configuration options in GBrowse.
For the main GBrowse configuration article, see: GBrowse Configuration.
This is declaring a new constant track in the overview named “SNP Density.” The feature is “snp_density”, corresponding to the aggregator declared earlier. The glyph is “xyplot” using the graph type of “boxes” to generate a column graph.
To set up a track so that the histogram appears when the user zooms out beyond 100,000 bp but shows the detailed information at higher magnifications, generate two track sections like these:
[SNPs]
feature = snp
glyph = triangle
point = 1
orient = N
height = 6
bgcolor = blue
fgcolor = blue
key = SNPs
[SNPs:100000]
feature = snp_density
glyph = xyplot
graph_type = boxes
scale = right
The first track section sets up the defaults for the SNP track. SNPs are represented as blue triangles pointing North. The second track declaration declares that when the user zooms out to over 100K base pairs, GBrowse should display the snp_density feature using the xyplot glyph.