During the summer of 2010 I worked as a research intern in the Bioinformatics Laboratory at Ohio University in Athens, OH.
My work was on the visualization of relationships between methylation levels in cancerous ovarian cells and normal ovarian cells. This repo serves as a summary of my contributions and collaborations during that time:
A Perl module used to show relationships between n nodes in k sets with a set of edges of varying types; output as a PNG image.
A Perl module that expands on the capabilities of the Graph module above, but outputs as an interactive Scalable Vector Graphic (SVG).
The Graph/SVG module allows node sets and edge sets to be defined by an external style sheet. svg_default.style defines the default style when no other file is provided.
To define the properties of a set of nodes:
set:
name: default
node-fill: rgb(255, 0, 0)
node-alpha: 0.1
node-stroke-color: rgb(0, 0, 0)
node-stroke-width: 1
node-radius: 10
To define the properties of a set of edges:
edge:
name: default
color: rgb(0, 0, 0)
dashed: false
I developed this module towards the end of my internship so I did not have a chance to run the cell methylation data or motif data through it, however, a usage example script and a couple sample SVG output images are included in ./svg.
A Perl script that uses perl-modules/Graph to generate PNG images visualizing the relationships between cancerous and normal ovarian cells. The input data has been redacted as it is not mine to distribute, but a few sample result images have been included in methylation/results.
Ex.
A Perl script that uses perl-modules/Graph to visualize DNA word clusters (motifs) identified in Regulatory Network Nodes of Check Point Factors in DNA Repair Pathways.
The resulting visualization:
