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BIRL / ATLANTIS

An Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming
http://biolabs.lums.edu.pk/birl
GNU General Public License v3.0
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Is it possible to get access to XYZ plot coordinates? #2

Open jpcartailler opened 5 years ago

jpcartailler commented 5 years ago

Greetings,

We have been exploring a boolean network using ATLANTIS and are wanting to better control some of the plots. Specifically, as shown in https://www.nature.com/articles/s41598-018-22031-3/figures/3 (panel D): image Would it be possible for ATLANTIS to export the XYZ coordinates (and peak annotations) alongside of the plots? This would permit us (and others) to better visualize the output, especially for those who are running network perturbations and wish to visual peak variance between conditions.

Thanks for any info, ideas and such. We're happy to get our fingers dirty, but perhaps there's something in place that simply needs to be exposed.

BIRL commented 5 years ago

Dear Osama,

Please guide JP Cartellier on how to download the mesh data from the plot (figure). In case you feel a need to discuss it, lets set up a skype.

Best, Safee

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On Tue, Aug 27, 2019 at 8:10 AM JP Cartailler notifications@github.com wrote:

Greetings,

We have been exploring a boolean network using ATLANTIS and are wanting to better control some of the plots. Specifically, as shown in https://www.nature.com/articles/s41598-018-22031-3/figures/3 (panel D): [image: image] https://user-images.githubusercontent.com/5258731/63737989-e619d380-c84d-11e9-8e0a-013b44d07416.png Would it be possible for ATLANTIS to export the XYZ coordinates (and peak annotations) alongside of the plots? This would permit us (and others) to better visualize the output, especially for those who are running network perturbations and wish to visual peak variance between conditions.

Thanks for any info, ideas and such. We're happy to get our fingers dirty, but perhaps there's something in place that simply needs to be exposed.

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osamashiraz commented 5 years ago

Hi JP,

Would it be possible for ATLANTIS to export the XYZ coordinates (and peak annotations) alongside of the plots?

I modified some m files to output grid data. First you will have to replace following ATLANTIS.zip in your current ATLANTIS DIR (perhaps make a copy). Then put debugger on ATLANTIS.m line 838 if running single network analysis or line 921 if running multiple network analyses. When you evaluate _[errormsg2 , finishTime, figHandle, gridToolTipData, gridData] = generateAttractorLandscape", gridData should have information on XYZ values.

I could not test these files but they should work. If something does not work do let me know, I will try my best to help.

Best Osama

jpcartailler commented 5 years ago

Dear Osama & Safee - thank you both for the fast response and solution. I will follow-up with the outcome on our end, hopefully later this week. Many, many thanks! JP

jpcartailler commented 5 years ago

Quick update - we've following Osama's instructions but I'm not sure we're doing it correctly.

  1. Made a backup of our Atlantis install
  2. Extracted ZIP file as instructed, overwriting some original files
  3. Added a debugger on line 838
  4. Ran a sample analysis and select to plot a PEL from the visualization option.
  5. Selected and evaluated [errormsg2 , finishTime, figHandle, gridToolTipData, gridData] = generate_AttractorLandscape and got the following workspace output image
  6. In addition, we see the plot actually get plotted. However, the gridData workspace object appears to be empty, or is it that we're looking in the wrong place for it?

Thanks! JP

BIRL commented 5 years ago

Dear Osama,

Please look into why gridData might be empty.

Best, Safee

On Mon, Sep 16, 2019 at 9:16 PM JP Cartailler notifications@github.com wrote:

Quick update - we've following Osama's instructions but I'm not sure we're doing it correctly.

  1. Made a backup of our Atlantis install
  2. Extracted ZIP file as instructed, overwriting some original files
  3. Added a debugger on line 838
  4. Ran a sample analysis and select to plot a PEL from the visualization option.
  5. Selected and evaluated [errormsg2 , finishTime, figHandle, gridToolTipData, gridData] = generate_AttractorLandscape and got the following workspace output [image: image] https://user-images.githubusercontent.com/5258731/64974698-f16f8600-d872-11e9-8ff3-80df177cf6c0.png
  6. In addition, we see the plot actually get plotted. However, the gridData workspace object appears to be empty, or is it that we're looking in the wrong place for it?

Thanks! JP

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-- Safee Ullah Chaudhary, Ph.D. | Assistant Professor, Biomedical Informatics Research Laboratory (BIRL), Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan Voice: +92 42 3560 8352 | Cell: +92 321 4255171 | Fax: +92 42 3560 8317 Email: safeeullah@lums.edu.pk, chaudhary.safee.ullah.2018@gmail.com chaudhary.safee.ullah@gmail.com Web: biolabs.lums.edu.pk/BIRL

osamashiraz commented 5 years ago

Hi JP,

This was not expected. Could you add a debugger in the generate_AttractorLandscape.m itself at line 265. If you see lines 268, 282, and 292 there will be three attractor landscape plotting functions. Depending on your choice, the corresponding plot function will be called. Could you check if you can get the grid data directly from this function.

Let me know if this works for you.

Best Osama

On Mon, Sep 16, 2019 at 12:36 PM Biomedical Informatics Research Laboratory notifications@github.com wrote:

Dear Osama,

Please look into why gridData might be empty.

Best, Safee

On Mon, Sep 16, 2019 at 9:16 PM JP Cartailler notifications@github.com wrote:

Quick update - we've following Osama's instructions but I'm not sure we're doing it correctly.

  1. Made a backup of our Atlantis install

  2. Extracted ZIP file as instructed, overwriting some original files

  3. Added a debugger on line 838

  4. Ran a sample analysis and select to plot a PEL from the visualization option.

  5. Selected and evaluated [errormsg2 , finishTime, figHandle, gridToolTipData, gridData] = generate_AttractorLandscape and got the following workspace output [image: image] < https://user-images.githubusercontent.com/5258731/64974698-f16f8600-d872-11e9-8ff3-80df177cf6c0.png

  6. In addition, we see the plot actually get plotted. However, the gridData workspace object appears to be empty, or is it that we're looking in the wrong place for it?

Thanks! JP

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/BIRL/ATLANTIS/issues/2?email_source=notifications&email_token=ACARXW56XFKH54VGUF6IEXTQJ6WMLA5CNFSM4IP3LOE2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6ZV73I#issuecomment-531849197 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ACARXW3XBEUVFYS5KYZUEZLQJ6WMLANCNFSM4IP3LOEQ

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-- Safee Ullah Chaudhary, Ph.D. | Assistant Professor, Biomedical Informatics Research Laboratory (BIRL), Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan Voice: +92 42 3560 8352 | Cell: +92 321 4255171 | Fax: +92 42 3560 8317 Email: safeeullah@lums.edu.pk, chaudhary.safee.ullah.2018@gmail.com chaudhary.safee.ullah@gmail.com Web: biolabs.lums.edu.pk/BIRL

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-- Regards, Osama Shiraz

jpcartailler commented 5 years ago

Hi again and thanks for the additional suggestion. We tried it (for plotPEL and plotPL) within the generate_AttractorLandscape.m and we do not see any value for gridData.

image