Saving a Galaxy visualization (e.g. PNG or PDF) into the history / workflow

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Saving a Galaxy visualization (e.g. PNG or PDF) into the history / workflow

Peter Cock
Hello all,

I'm hoping to construct a workflow which produces a simple tally table
(using the "Count1" tool, "Count occurrences of each record", which is
still shipped with the Galaxy core) and then draws this as a Pie Chart.

1. Using "Count1", generate tally table (a simple two column tabular file,
counts and labels as c1 and c2) in the history.

2. Click on the tally table in the history to expand the green box

3. Click on the "Visualize" icon, pick "Charts", click on "Pie Chart"

4. Click "Draw" or the "Configuration" tab.

5. Change donut ratio to zero, show legend to true, and show labels
output to true.

6. Click "Draw" or the "Add Data" tab.

7. Under "Select Columns", "Labels", pick c2

8. Under "Select Columns", "Values", keep default c1

9. Click "Draw"

10. Admire interactive Pie Chart

11. Click "Screenshot", offered PNG / SVG / PDF but these are
only direct downloads (well, PDF is more complicated).

Question: How can I "save" a static snapshot of the Pie Chart as a
new history item (other than downloading it locally and then uploading
it)?

Question: If so, can I then turn this history into a workflow which
would recreate the pie chart?

As a work around I could write a traditional Galaxy tool which takes
as input data files(s) and pre-sets the columns and visualisation
settings, and produces static image(s) as output (e.g. PDF and PNG).

Peter
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Re: Saving a Galaxy visualization (e.g. PNG or PDF) into the history / workflow

Peter Cock
On Tue, Mar 10, 2015 at 11:24 AM, Peter Cock <[hidden email]> wrote:

> Hello all,
>
> I'm hoping to construct a workflow which produces a simple tally table
> (using the "Count1" tool, "Count occurrences of each record", which is
> still shipped with the Galaxy core) and then draws this as a Pie Chart.
>
> 1. Using "Count1", generate tally table (a simple two column tabular file,
> counts and labels as c1 and c2) in the history.
>
> 2. Click on the tally table in the history to expand the green box
>
> 3. Click on the "Visualize" icon, pick "Charts", click on "Pie Chart"
>
> 4. Click "Draw" or the "Configuration" tab.
>
> 5. Change donut ratio to zero, show legend to true, and show labels
> output to true.
>
> 6. Click "Draw" or the "Add Data" tab.
>
> 7. Under "Select Columns", "Labels", pick c2
>
> 8. Under "Select Columns", "Values", keep default c1
>
> 9. Click "Draw"
>
> 10. Admire interactive Pie Chart
>
> 11. Click "Screenshot", offered PNG / SVG / PDF but these are
> only direct downloads (well, PDF is more complicated).
>
> Question: How can I "save" a static snapshot of the Pie Chart as a
> new history item (other than downloading it locally and then uploading
> it)?
>
> Question: If so, can I then turn this history into a workflow which
> would recreate the pie chart?
>
> As a work around I could write a traditional Galaxy tool which takes
> as input data files(s) and pre-sets the columns and visualisation
> settings, and produces static image(s) as output (e.g. PDF and PNG).
>
> Peter

I should add that I've tried this on both the latest Galaxy from GitHub
running locally as my development server, and with the current stable
release at http://usegalaxy.org

Also the "Screenshot" button has a camera icon (makes sense). I'd
like a "Save" button (using the disk icon) as well or instead. Meanwhile
the "Draw" button (used in steps 4, 6, 9) has a disk icon which seems
somewhat confusing to me (it doesn't save - it takes you to another
interactive page within Galaxy).

Peter
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Re: Saving a Galaxy visualization (e.g. PNG or PDF) into the history / workflow

Carl Eberhard
In short:
 
Question: How can I "save" a static snapshot...?
You can't yet.

Question: If so, can I then ...recreate the pie chart?
No, not yet.

Overall, these are features that we definitely want and we are working towards them. Questions remain for me, if I understand your original questions, about these two features.

Re: saving a visualization to a history: 
  • What is the final use of the 'hardcopy' (png or pdf) of the visualization? In other words, is it for: publication or exposition, summary/overview info, a jumping off point for exploring the data, or something else?
  • Isn't this an artifact (a view or byproduct) of the analysis and not actually a dataset itself?
  • Do you want a static version or, if possible, easier access to a pre-configured interactive visualization?
  • Would a saved visualization (of the type you find under 'Visualizations->Saved Visualizations' menu) work in a png or pdf's place?
In any event, I think more flexible conversion of visualizations to hardcopies is doable with some added backend technology like ImageMagick to render SVG to PNG, etc. If also wrapped in a tool, this would let us add these to the history.

Re: generating a visualization from a workflow:
  • Would a saved visualization work here as well?

I think the main problem here is translation of what may be a more complex visualization UI (to control the configuration) to something that can be more simply rendered in a workflow page (as tool configurations are now). At least some of the configuration could be handled this way, at any rate - things like Chart's chart type, and data columns, etc. 

There are ways to pass visualization configurations directly over the url, so this may be easier than I think too.

These are good ideas. Thanks, Peter.


On Tue, Mar 10, 2015 at 7:46 AM, Peter Cock <[hidden email]> wrote:
On Tue, Mar 10, 2015 at 11:24 AM, Peter Cock <[hidden email]> wrote:
> Hello all,
>
> I'm hoping to construct a workflow which produces a simple tally table
> (using the "Count1" tool, "Count occurrences of each record", which is
> still shipped with the Galaxy core) and then draws this as a Pie Chart.
>
> 1. Using "Count1", generate tally table (a simple two column tabular file,
> counts and labels as c1 and c2) in the history.
>
> 2. Click on the tally table in the history to expand the green box
>
> 3. Click on the "Visualize" icon, pick "Charts", click on "Pie Chart"
>
> 4. Click "Draw" or the "Configuration" tab.
>
> 5. Change donut ratio to zero, show legend to true, and show labels
> output to true.
>
> 6. Click "Draw" or the "Add Data" tab.
>
> 7. Under "Select Columns", "Labels", pick c2
>
> 8. Under "Select Columns", "Values", keep default c1
>
> 9. Click "Draw"
>
> 10. Admire interactive Pie Chart
>
> 11. Click "Screenshot", offered PNG / SVG / PDF but these are
> only direct downloads (well, PDF is more complicated).
>
> Question: How can I "save" a static snapshot of the Pie Chart as a
> new history item (other than downloading it locally and then uploading
> it)?
>
> Question: If so, can I then turn this history into a workflow which
> would recreate the pie chart?
>
> As a work around I could write a traditional Galaxy tool which takes
> as input data files(s) and pre-sets the columns and visualisation
> settings, and produces static image(s) as output (e.g. PDF and PNG).
>
> Peter

I should add that I've tried this on both the latest Galaxy from GitHub
running locally as my development server, and with the current stable
release at http://usegalaxy.org

Also the "Screenshot" button has a camera icon (makes sense). I'd
like a "Save" button (using the disk icon) as well or instead. Meanwhile
the "Draw" button (used in steps 4, 6, 9) has a disk icon which seems
somewhat confusing to me (it doesn't save - it takes you to another
interactive page within Galaxy).

Peter
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: Saving a Galaxy visualization (e.g. PNG or PDF) into the history / workflow

Peter Cock
On Fri, Mar 13, 2015 at 3:31 PM, Carl Eberhard <[hidden email]> wrote:

> In short:
>
>>
>> Question: How can I "save" a static snapshot...?
>
> You can't yet.
>
>> Question: If so, can I then ...recreate the pie chart?
>
> No, not yet.
>
> Overall, these are features that we definitely want and we are working
> towards them. Questions remain for me, if I understand your original
> questions, about these two features.
>
> Re: saving a visualization to a history:
>
> What is the final use of the 'hardcopy' (png or pdf) of the visualization?
> In other words, is it for: publication or exposition, summary/overview info,
> a jumping off point for exploring the data, or something else?

In general I'm picturing the figure as one of several outputs from
a workflow - which could be intended as figures in a PDF paper.

In this specific example, the pie chart is essentially a visual summary
of a (crude) assembly contamination assessment.

I would be happy with a read-only static Pie Chart (as an easy to
download PNG/PDF).

If it remained an interactive image (from which I can still download
a PNG/PDF snapshot as now) that would be even more powerful,
but would not be a self-contained Galaxy dataset anymore.

> Isn't this an artifact (a view or byproduct) of the analysis and not
> actually a dataset itself?

I think from the way you are using the terms, I am thinking of a
saved visualisation as a Galaxy dataset in its own right.

> Do you want a static version or, if possible, easier access to a
> pre-configured interactive visualization?

A static image is fine. A pre-configured interactive visualization
would be good too - either as long it is an integral part of the
history/workflow, and would be shared along with it.

> Would a saved visualization (of the type you find under
> 'Visualizations->Saved Visualizations' menu) work in a png
> or pdf's place?

Possibly - how currently can the user save a visualization?

> In any event, I think more flexible conversion of visualizations to
> hardcopies is doable with some added backend technology like
> ImageMagick to render SVG to PNG, etc. If also wrapped in a
> tool, this would let us add these to the history.

That sounds good.

> Re: generating a visualization from a workflow:
>
> Would a saved visualization work here as well?

Yes, for me at least.

> I think the main problem here is translation of what may be a more complex
> visualization UI (to control the configuration) to something that can be
> more simply rendered in a workflow page (as tool configurations are now). At
> least some of the configuration could be handled this way, at any rate -
> things like Chart's chart type, and data columns, etc.

That's what I was hoping.

> There are ways to pass visualization configurations directly over the url,
> so this may be easier than I think too.
>
> These are good ideas. Thanks, Peter.

No problem - I'm glad to know the team are already working
towards this kind of functionality, even if we're not there yet.

Regards,

Peter
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/