[HN Gopher] Circos - Circular Visualization
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Circos - Circular Visualization
Author : smartmic
Score : 157 points
Date : 2024-07-09 11:44 UTC (1 days ago)
(HTM) web link (circos.ca)
(TXT) w3m dump (circos.ca)
| inciampati wrote:
| It's a nice visualization system when you have a lot of very long
| one-dimensional things with nonlinear relationships. This is
| super common in genomics but in principle could be applied many
| places.
|
| That said, circos plots are sort of cliche in genomics and I do
| see people tending to move away from them.
|
| It suffers from an effect of having too many things all together,
| all at once, layered in ways that sometimes make it difficult to
| compare. This is especially true when you have data tracks that
| are circularly laid out around the plot.
| aorth wrote:
| Came to say something similar. I've been installing and
| updating Circos on our HPC cluster for bioinformatics users for
| over ten years. It was really popular in the early and mid
| 2010s!
| mbreese wrote:
| I have used circos plots many times in the past (genomics).
| They make for very pretty figures. But, like you said, the
| major problem with them is that they are difficult to
| accurately interpret. They are used often to compare whole
| genome rearrangements, but the resolution has to be reduced to
| so much that you just can't use them quantitatively. They are
| useful for qualitative comparisons, but it really suffers when
| you need to show details.
| a_bonobo wrote:
| Yes, but they are pretty.
|
| Case in point: the maize genome Circos plot popped up in
| Jurassic World, they just overlayed an image of a Triceratops
| https://circos.ca/images/mastheads/
| tetris11 wrote:
| Yep, if you want to compare clusters from sample A with
| clusters from sample B, then it's just easier to use a sankey
| diagram, especially for time-series data.
| lbeltrame wrote:
| I don't get the fad with circos plots. At least in genomics, they
| offer a high density of information but unfortunately at the
| price of hard if not impossible interpretation. Like the systems
| biology papers of old, showing beautiful dense graphs, but with
| little room for biological interpretation. In addition, circos is
| quite... peculiar as an application, in particular its quirky
| configuration file format, which is half ini like and half XML or
| HTML like. Last I looked at it, about a decade ago, there weren't
| any APIs to create plots programmatically.
| munificent wrote:
| I've seen these circular plots a number of times and I've never
| once found them to illuminate the underlying data, even a little
| bit.
| esafak wrote:
| Maybe it is because you need to become used to them? I do not
| find them informative either.
| risenshinetech wrote:
| I came here to say the same thing. What insight do these
| diagrams provide? They always struck me as a useless but flashy
| visualization that you would put in front of your company to
| make people believe Important Work is happening inside.
| mmastrac wrote:
| I really struggle to understand most of the diagrams on this page
| without context. I suspect it's a lot more useful if you spend
| time swapping in the overall context of a diagram, after which
| you can visually pattern match. Without context, it's just pretty
| noise to me, IMO.
| zazaulola wrote:
| These charts remind me of astrologers' natal charts.
| cedricbonhomme wrote:
| I used Circos quite a lot back in time. It's written in Perl. I
| was working on a Python visualization tool for analyzing the
| relationships between different IP, from network traffic capture:
|
| https://github.com/cedricbonhomme/IP-Link
|
| (there is a link to the documentation with some nice chord
| diagrams.) This one is quite impressive:
| https://github.com/cedricbonhomme/IP-Link/blob/master/docs/_...
| nut not easy to read !
| robbles wrote:
| Doesn't this suffer from similar issues to a pie chart?
|
| e.g. https://scc.ms.unimelb.edu.au/resources/data-
| visualisation-a...
|
| I'm kinda suspicious that any data visualization that uses a
| circle is going to be hard to draw meaning from.
| ma2t wrote:
| Yes and no. When trying to show quantitative data in terms of
| areas or angles, then you are spot-on: same issues. But these
| plots, or chord diagrams more generally, are often used to show
| relationships (like translocations, inversions or duplications
| in genomes) in context of other landmarks. This use is common
| and less troublesome. A real problem with Circos plots is that
| it's so tempting to keep adding additional tracks of
| "information" that plots get ridiculous. It becomes like
| staring at the Voynich manuscript: uninterpretable but so
| compellingly pretty it must mean _something_.
| bee_rider wrote:
| Are pie charts bad or just misused?
|
| They aren't good at measuring small quantities. But it is easy
| to see 1/4 or 1/2 of a circle. And it is easy to see if
| something is a straight line, 90 degree, or a little more or
| less than either of those.
|
| Compared to a bar graph, it seems a little easier to spot that
| one quantity is, like, half of another. And it is easier to
| visually sum of a collection of quantities, on a bar graph this
| is a major pain (unless it is stacked of course but that's
| another type of graph).
| Vaslo wrote:
| Just feels like an overloaded chart where you can pick out maybe
| one to two patterns that are useful, similar to a pie chart
| showing maybe one to two chunks that overwhelm.
| dangets wrote:
| These types of graphs are also possible using D3.js. The "Chord
| diagam II" example references Circos implementation -
| https://observablehq.com/@d3/chord-diagram/2?intent=fork
| diekhans wrote:
| Circos is useful when the data is sparse and quickly becomes
| extremely time-consuming to near-impossible to interpret. The
| most you can say is "wow, there is a lot going on".
|
| I know in five seconds if a Circos plot is worth looking at.
| photonthug wrote:
| The same guy apparently made https://hiveplot.com/
| runlaszlorun wrote:
| Interesting link. I can't speak to the informational value of
| those hiveplot charts, but an interesting piece from the author
| on the merits of different network visualization approaches.
| anigbrowl wrote:
| This is highly relevant to my interests, thanks
| anigbrowl wrote:
| Longtime fan of this project. Genomics is where the interesting
| UI design in science is at, and it's quite useful for others
| things outside of genomics. Most dashboards are garbage by
| comparison.
| breck wrote:
| Interesting.
|
| Does anyone have a link to a particularly amazing circos chart
| that demonstrates the kind of story that it is best at conveying?
| sumnole wrote:
| One of my favorite circular data viz plots is the polar diagram.
| It's a simple plot but leads to some pretty aesthetic and easy to
| read results.
| motohagiography wrote:
| radial dendrograms are great for looking at differences between
| clusters of relationships in trees. thanks for this tool, making
| viz tools accessible will refine their use cases. one of the
| challenges with viz is matching the message with the viewer.
|
| re some of the viz comments here, most sankey diagrams can be pie
| charts (any one with less than a few nested categories) and most
| people who make pie charts don't reason about trees so all the
| junk sankey diagrams that flooded in after the birthday party
| chart aren't a reflection of their use or value.
|
| messages I've used viz for in the past were to solve problems
| like:
|
| - these things are similar and different (heatmap)
|
| - this is a bounded domain (digraph/ontology)
|
| - these things are related, but only relative to these other
| things (graph clusters, radial/linear network diagram,
| boxes+lines/nested boxes)
|
| - the complexity is more here than there (graph clusters)
|
| - the taxonomy hides an inconsistency or gap (sankey diagrams)
|
| - either everybody sees this or nobody does (graph clusters)
|
| - these variations cause combinatoric explosion (sankey diagram)
|
| - this is a hierarchy (dendrogram, radial dendrogram)
|
| - these are categories of things (dendrogram, radial dendrogram)
|
| - these things are the same (heatmap)
|
| - start with these to have the most effect on those (cluster
| graph)
|
| - solutions are in the form of this grammar (sankey diagram)
|
| - these things happen in order (state machine/flow chart, gantt
| chart)
|
| - these things happen together (gantt chart)
|
| The statements may seem naive, but when you're working on a viz,
| you have to think about who it is for and whether it is the right
| representation and whether the message is valuable. I've made a
| lot of viz mistakes and they came down to not framing one of
| these messages correctly or misunderstanding how telling someone
| this would make them feel. the radial diagrams are pretty, and
| very useful for showing contrast between patterns and density of
| relationships.
| Uehreka wrote:
| This looks neat, but as a dataviz person who works on the web, my
| first question (which I couldn't find an answer to, though I was
| skimming) is why would I use a special-purpose tool for these
| kinds of charts when D3 already supports these kinds of charts
| pretty thoroughly, allows me to update data in realtime and
| supports animation. Plus D3 can render to either SVG or canvas,
| it even supports offline rendering for creating vector-based
| charts for print purposes.
| Blahah wrote:
| Circos.js uses d3 and works great with other things in the
| ecosystem. You customise it with idiomatic d3.
| dolmen wrote:
| The Circos authors invented those charts. D3 got another
| implementation later.
|
| https://genome.cshlp.org/content/early/2009/06/15/gr.092759....
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