Jalview PCA?

Hi,

I was wondering how does Jalview calculate the aligned sequence to generate PCA plot? and also it is possible to find a source code so I can use the same function/calculation to make similar plots? such as if I want to present it in 2D PCA, or applied in onto different visualisation algorithm…?
The PCA of Jalview is great but I was hoping if it could be more friendly for higher quality and flexibility in terms of publication.

Thanks,

Yang Cheng

This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.

The pca page on jalview.org is pretty descriptive. Such that you can fairly easily replicate in R using the ape package.

http://www.jalview.org/help/html/calculations/pca.html

···

Sent from my Samsung Galaxy smartphone.

-------- Original message --------
From: Cheng Yang cheng_yang@immunol.a-star.edu.sg
Date: 24/06/2017 05:39 (GMT+00:00)
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Jalview PCA?

Hi,

I was wondering how does Jalview calculate the aligned sequence to generate PCA plot? and also it is possible to find a source code so I can use the same function/calculation to make similar plots? such as if I want to present it in 2D PCA, or applied in onto different visualisation algorithm…?
The PCA of Jalview is great but I was hoping if it could be more friendly for higher quality and flexibility in terms of publication.

Thanks,

Yang Cheng

This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.

The University of Dundee is a registered Scottish Charity, No: SC015096

Hello Cheng,

Jalview source is available from http://www.jalview.org/development/development-builds or at https://source.jalview.org/crucible/browse/~br=develop/jalview/. Jalview is open source under GPL licence (see http://www.jalview.org/).

If you are keen to look at the code, I would on this occasion point you to the ‘develop’ branch. This includes a restructured version of the PCA calculation, with greatly improved speed and memory performance, which will be included in the next Jalview release (coming shortly). But please note that ‘develop’ is subject to change, and the stable version will be the one with tag “Release_2_10_2” once released.

The files to look at are:

For the calculation:

jalview.analysis.PCA.run()

  • overall control of the calculation

jalview.analysis.scoremodels.ScoreMatrix.findSimilarities()

  • computes sequence similarities using the supplied score model (e.g. Blosum62)

  • folder resources/scoreModel has files with substitution matrix data

jalview.gui.CalculationChooser.getSimilarityParameters()

  • sets parameters that condition the similarity calculation

jalview.math.Matrix.tred(), tqli()

  • perform matrix calculations required for the PCA algorithm

For the display:

jalview.viewmodel.PCAModel.run()

  • retrieves calculated values for the display

jalview.gui.PCAPanel.run()

  • renders the PCA to the screen

We’d be interested to know what you had in mind under “more friendly for higher quality and flexibility in terms of publication”, as we are always looking for ways to make Jalview more useful!

Best regards,

Mungo

···

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Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

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From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of David Booth (Staff) d.z.booth@dundee.ac.uk
Sent: 24 June 2017 13:14:06
To: Cheng Yang; jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] Jalview PCA?

The pca page on jalview.org is pretty descriptive. Such that you can fairly easily replicate in R using the ape package.

http://www.jalview.org/help/html/calculations/pca.html

Sent from my Samsung Galaxy smartphone.

-------- Original message --------
From: Cheng Yang cheng_yang@immunol.a-star.edu.sg
Date: 24/06/2017 05:39 (GMT+00:00)
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Jalview PCA?

Hi,

I was wondering how does Jalview calculate the aligned sequence to generate PCA plot? and also it is possible to find a source code so I can use the same function/calculation to make similar plots? such as if I want to present it in 2D PCA, or applied in onto different visualisation algorithm…?
The PCA of Jalview is great but I was hoping if it could be more friendly for higher quality and flexibility in terms of publication.

Thanks,

Yang Cheng

This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.

The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096