Added a Log scale toggle to the Wiggle track menu #502

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hotdogee commented Aug 19, 2014

The design is that when Log scale is toggled on, the mouse over pixel values still display the original value.

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I feel like there are not many tracks where you would want to view both log scale and regular scale. Is there any particular reason for this?

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cmdcolin commented Feb 6, 2015

I feel like there are not many tracks where you would want to view both log scale and regular scale. Is there any particular reason for this?

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Only seems useful in case someone is opening their own data, but even still this seems to me to be sort of a "next-gen graphical configuration" type option

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cmdcolin commented Feb 6, 2015

Only seems useful in case someone is opening their own data, but even still this seems to me to be sort of a "next-gen graphical configuration" type option

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childers Feb 6, 2015

Hi Colin,

It can help to show relatively low signal when nearby areas have higher
expression. When zoomed in sufficiently, the scale should redraw. This is
especially useful when zoomed out, as sometimes high expressed regions are
near lower expressed genes.

Take a look at the following view, and toggle the log view on and off to
see what I mean. When zoomed in, you can clearly see the signal, but when
zoomed out, the last exon of the leftmost gene sets the scale so high the
rest of it looks like background.

https://apollo.nal.usda.gov/anogla/jbrowse/?loc=Scaffold1%3A2699561..2721160&tracks=DNA%2CAnnotations%2Canogla_current_models%2CAgla_RNA-female_bigwig%2CAgla_RNA-male_bigwig&highlight=

On Fri, Feb 6, 2015 at 1:43 PM, Colin Diesh notifications@github.com
wrote:

Only seems useful in case someone is opening their own data, but even
still this seems to me to be sort of a "next-gen graphical configuration"
type option


Reply to this email directly or view it on GitHub
#502 (comment).

childers commented Feb 6, 2015

Hi Colin,

It can help to show relatively low signal when nearby areas have higher
expression. When zoomed in sufficiently, the scale should redraw. This is
especially useful when zoomed out, as sometimes high expressed regions are
near lower expressed genes.

Take a look at the following view, and toggle the log view on and off to
see what I mean. When zoomed in, you can clearly see the signal, but when
zoomed out, the last exon of the leftmost gene sets the scale so high the
rest of it looks like background.

https://apollo.nal.usda.gov/anogla/jbrowse/?loc=Scaffold1%3A2699561..2721160&tracks=DNA%2CAnnotations%2Canogla_current_models%2CAgla_RNA-female_bigwig%2CAgla_RNA-male_bigwig&highlight=

On Fri, Feb 6, 2015 at 1:43 PM, Colin Diesh notifications@github.com
wrote:

Only seems useful in case someone is opening their own data, but even
still this seems to me to be sort of a "next-gen graphical configuration"
type option


Reply to this email directly or view it on GitHub
#502 (comment).

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Ya. I can see that, it looks pretty good there too. I think this is probably fine to merge then. It would be cool if the scale bar was actually "log scaled" i.e. 1. 10. 100 though

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cmdcolin commented Feb 6, 2015

Ya. I can see that, it looks pretty good there too. I think this is probably fine to merge then. It would be cool if the scale bar was actually "log scaled" i.e. 1. 10. 100 though

cmdcolin added a commit that referenced this pull request Feb 6, 2015

Merge pull request #502 from hotdogee/wiggle-log-scale
Added a Log scale toggle to the Wiggle track menu

@cmdcolin cmdcolin merged commit 7c48e9d into GMOD:master Feb 6, 2015

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Just as a note: I made this an optional configuration item

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cmdcolin commented Feb 9, 2015

Just as a note: I made this an optional configuration item

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selewis Feb 10, 2015

Hi Colin,

I don't think it should merely be a configuration item (though that may be
the best way to start). It should be something the user can toggle for the
track, to switch between them (though perhaps this is handled via dynamic
configuration?)

On Mon, Feb 9, 2015 at 10:14 PM, Colin Diesh notifications@github.com
wrote:

Just as a note: I made this an optional configuration item


Reply to this email directly or view it on GitHub
#502 (comment).

selewis commented Feb 10, 2015

Hi Colin,

I don't think it should merely be a configuration item (though that may be
the best way to start). It should be something the user can toggle for the
track, to switch between them (though perhaps this is handled via dynamic
configuration?)

On Mon, Feb 9, 2015 at 10:14 PM, Colin Diesh notifications@github.com
wrote:

Just as a note: I made this an optional configuration item


Reply to this email directly or view it on GitHub
#502 (comment).

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This pull request was actually for creating the easy toggle checkbox for turning on log scale. Here is how it looks:

screenshot-localhost 2015-02-09 19-12-22

My concern was that "well, not everyone might want that checkbox" so I made it optional.

Then I only enabled it on one example track in the sample browser.

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cmdcolin commented Feb 10, 2015

This pull request was actually for creating the easy toggle checkbox for turning on log scale. Here is how it looks:

screenshot-localhost 2015-02-09 19-12-22

My concern was that "well, not everyone might want that checkbox" so I made it optional.

Then I only enabled it on one example track in the sample browser.

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selewis Feb 10, 2015

Nope, everyone will want it, for exactly the reasons that Chris described.
Doesn't need to be optional, preferably shouldn't be.

On Tue, Feb 10, 2015 at 1:14 AM, Colin Diesh notifications@github.com
wrote:

This pull request was actually for creating the easy toggle checkbox for
turning on log scale. Here is how it looks:

[image: screenshot-localhost 2015-02-09 19-12-22]
https://cloud.githubusercontent.com/assets/6511937/6119547/b32521b2-b08f-11e4-9556-4f12747b511b.png

My concern was that "well, not everyone might want that checkbox" so I
made it optional.

Then I only enabled it on one example track in the sample browser.


Reply to this email directly or view it on GitHub
#502 (comment).

selewis commented Feb 10, 2015

Nope, everyone will want it, for exactly the reasons that Chris described.
Doesn't need to be optional, preferably shouldn't be.

On Tue, Feb 10, 2015 at 1:14 AM, Colin Diesh notifications@github.com
wrote:

This pull request was actually for creating the easy toggle checkbox for
turning on log scale. Here is how it looks:

[image: screenshot-localhost 2015-02-09 19-12-22]
https://cloud.githubusercontent.com/assets/6511937/6119547/b32521b2-b08f-11e4-9556-4f12747b511b.png

My concern was that "well, not everyone might want that checkbox" so I
made it optional.

Then I only enabled it on one example track in the sample browser.


Reply to this email directly or view it on GitHub
#502 (comment).

cmdcolin added a commit that referenced this pull request Feb 10, 2015

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childers Feb 10, 2015

Thanks for the great discussion! I'm glad that this and #503 are merged in! I'll need to talk with @hotdogee about #504.

Thanks for the great discussion! I'm glad that this and #503 are merged in! I'll need to talk with @hotdogee about #504.

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