Question: Understanding the height in sashimi plots made by Gviz
gravatar for Leonardo Collado Torres
17 months ago by
United States
Leonardo Collado Torres590 wrote:


A colleague of mine asked me what the height in the sashimi plots created by Gviz represents. It was not intuitive and I dug around quite a bit before coming to the following conclusions:

* the height of an arc is not informative, it's just for graphical purposes. 

* the Y-axis on the sashimi arcs shows the relationship between the line width the the number of reads spanning a given junction.


Below is a screenshot of the Gviz 1.8.0 (Bioc 3.4 release) vignette. It's not initally clear why the arcs have different heights.

I did look at the vignette, the documentation, the sashimi plot paper and the code. Eventually I understood that the code at is for determining the height of the sashimi track (how much space is needed for the plot) and that the score (or scaled score) was not really used for that part since `.sashimi.junctions()` is called later on That's when I realized the meaning of the Y-axis label (which is not part of the original sashimi plot paper).

So, I just want to make sure that we got the interpretation correctly of the arc heights. If so, it'd be great if this information was described in the Gviz vignette (and maybe also the R docs).





ADD COMMENTlink modified 17 months ago by Robert Ivanek500 • written 17 months ago by Leonardo Collado Torres590
gravatar for Robert Ivanek
17 months ago by
Robert Ivanek500
Robert Ivanek500 wrote:

Hi Leo,

It is correct, I added the information into vignette. Sorry for not putting it there before.



ADD COMMENTlink written 17 months ago by Robert Ivanek500

Awesome, thank you for verifying my guess and for adding the information to the vignette. And no need to apologize, I know that documentation is a continuous process. Thanks again!

ADD REPLYlink written 16 months ago by Leonardo Collado Torres590
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