visualization of genomic data with the Hilbert curve
hilbertvis.sh $input $output $chromInfo "$chrom" $plot_value.score_col $level $mode
#if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__)
1 4 5 7
#else
${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol}
#end if
**Dataset formats**
The input format is interval_, and the output is an image in PDF format.
(`Dataset missing?`_)
.. _interval: ./static/formatHelp.html#interval
.. _Dataset missing?: ./static/formatHelp.html
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**What it does**
HilbertVis uses the Hilbert space-filling curve to visualize the structure of
position-dependent data. It maps the traditional one-dimensional line
visualization onto a two-dimensional square. For example, here is a diagram
showing the path of a level-2 Hilbert curve.
.. image:: ../static/images/hilbertvisDiagram.png
The shade of each pixel represents the value for the corresponding bin of
consecutive genomic positions, calculated according to the specified
summarization mode. The pixels are arranged so that bins that are close
to each other on the data vector are represented by pixels that are close
to each other in the plot. In particular, adjacent bins are mapped to
adjacent pixels. Hence, dark spots in a figure represent a peak; the area
of the spot in the two-dimensional plot is proportional to the width of the
peak in the one-dimensional data, and the darkness of the spot corresponds to
the height of the peak.
The input file is in interval format, and typically contains a column with
scores or other numbers, such as conservation scores, SNP density, the
coverage of aligned reads from ChIP-Seq data, etc.
Website: http://www.ebi.ac.uk/huber-srv/hilbert/
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**Examples**
Here are some examples from the HilbertVis homepage, using ChIP-Seq data.
.. image:: ../static/images/hilbertvis1.png
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.. image:: ../static/images/hilbertvis2.png
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**Reference**
Anders S. (2009)
Visualization of genomic data with the Hilbert curve.
Bioinformatics. 25(10):1231-5. Epub 2009 Mar 17.