Batch command: Autoscale

[LucasMichelTodo]

I can't manage to find the way to autoscale (or scale by any means) the tracks loaded in a batch file.

Thank you very much for the great work!

[jrobinso]

What have you tried, and what version of IGV are you using?

Responses will probably be delayed until next week, I am traveling.

[LucasMichelTodo]

Hi, thank you for the quick response!

I am currently using IGV v2.8.0 and I have tried the following with a .bdg file loaded:
preference CHART.AUTOSCALE TRUE
preference CHART.SHOW_DATA_RANGE TRUE

Thank's for letting me know you'll be out, I'm by no means in a hurry!

[jrobinso]

Sorry for the long delay. There was a command for setting the scale, but not documented, I am correcting that. Until now there was no way to set a track to autoscale, but most if not all track types autoscale by default. However I have explicitly added that option as shown below, which sets the first track to a scale of 0-50, and the second to auto. The 'auto' argument is part of the upcoming 2.11.0 release, the data range should work with previous releases.

new
genome hg19
goto chr1
load http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneA549H2azDex100nmSig.bigWig
load http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneA549H3k04me2Dex100nmSig.bigWig
setDataRange 0,50 wgEncodeBroadHistoneA549H2azDex100nmSig.bigWig
setDataRange auto wgEncodeBroadHistoneA549H3k04me2Dex100nmSig.bigWig

[jrobinso]

Doc has been updated. https://github.com/igvteam/igv/wiki/Batch-commands

[LucasMichelTodo]

Thank you very much for the reply and for this amazing software! I'll try it as soon as I get the time. Lucas Missatge de Jim Robinson ***@***.***> del dia dc., 4 d’ag. 2021 a les 5:08:

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[markgene]

Hi @jrobinso how to do group autoscale for multiple numeric tracks? Thanks!

[jrobinso]

@markgene Good question, that doesn't look possible with a batch command. Can you open a separate issue for that?

[markgene]

@jrobinso just created one #1178 Thank you, Jim!

@markgene Good question, that doesn't look possible with a batch command. Can you open a separate issue for that?