3 ms·

I've used datashader for plotting NGS (Next Generation Sequencing) enrichments. At the time I had to hack together the ability to use the polygon select tool o

by itodd 8y ago

I've used datashader for plotting NGS (Next Generation Sequencing) enrichments. At the time I had to hack together the ability to use the polygon select tool on the data, but it worked and blew my mind. Very elegant solution to a difficult problem (overplotting).

abcc8 8y ago
Do you have any examples of this you could point to online? I am looking at different visualization tools for various NGS-based analyses currently.
- itodd 8y ago
  I do. I remember posting this to the mailing list. I don't have an example calculating enrichments though. We simply group by read and divide using the frequencies and then plot one enrichment vs another. This way we can see how one sequence enriches between conditions. There's more to it than that but this will produce a plot similar to the one in the attachment in the thread linked below. https://groups.google.com/a/continuum.io/forum/m/#!msg/bokeh/BdQV54W0WnY/OHjlMAtqBAAJ https://groups.google.com/a/continuum.io/forum/m/#!msg/bokeh... Edit: here's a link to the plot I refer to: https://10826817673355204906.googlegroups.com/attach/e6e58ade6248/Screen%20Shot%202017-05-04%20at%202.47.07%20PM.png?part=0.1&view=1&vt=ANaJVrHL6xR_HvljfCodWVnBwALwADyL8wIpWga5D7Q5DzAHYPOsTTpqg193EuAC81xxXb-toP7Nv8y724yMogPSNlLXeU6lZXJ-Trm3r5-zpIVHEe2fpUI https://10826817673355204906.googlegroups.com/attach/e6e58ad...
deleted 8y ago
[deleted]