Sashimi plot track height

[PJ]

I'm using IGV 2.3.78 on MacOS 10.11.5

I've noticed a change in the way IGV displays the sashimi plots: the track height used to adjust automatically to the number of reads but for whatever reason, now it's always set up at 60. Similarly, some of the settings were maintained as long as I wouldn't restart IGV (for exmaple once I would set up the minimum number of reads to a certain number, that setting would be maintained, regardless of the gene I'm looking at), but again, for whatever reason, I have to set it up every time I look at a different gene.
Is there a way to change the defaults settings for the display of sashimi plots? I've looked in the preferences but couldn't find anything.
I also tried to reinstall IGV several times, but it didn't change anything. The default sashimi plot track height seems to be stuck at 60.

Any idea?

Thank you
PJ

[Jim Robinson]

I'll look into it.  When you say "track height" do you mean the Y axis scale, as opposed to actual height in pixels?

I've  opened an issue for this here: https://github.com/igvteam/igv/issues/287

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[Pierre-Jacques HAMARD]

Hi Jim

Yes, that's what I meant.

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[Jim Robinson]

Hi PJ,

Could you be more precise,  I have looked into this and am not seeing what you are seeing.  Perhaps some screenshots would help.   There are 2 max settings,  exon coverage and junction coverage,  neither are "60" for me and in fact the number 60 does not appear in the code. 

Also, which version of IGV are you comparing 2.3.78 to?

Jim

[Pierre-Jacques HAMARD]

Hi Jim

here are 2 screenshots: one to show the main window, the second showing the sashimi plot window.

as you can see, when I open the sashimi plot window, the tracks height is set up to 60. it used to be autoscale. but again, I can't find any option in the preferences to change that.

I think the last time it worked properly was with the 2.3.74, but I'm not sure. I know that at one point it stopped working so I started downloading the new versions and re-installing over and over again, thinking that perhaps this bug would get fixed in the newest versions.

What's weird is that even when I de-install everything (by trying to delete all the files that are related to IGV, like the preference files, the caches, etc...), and re-install the newest version, the sashimi plot window is still set up at 60.

PJ

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[Jim Robinson]

OK,  I'll compare with 2.3.74 and see what happened.  The best strategy to get bugs fixed is report them here or on github.

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