PCA custom coloring

Jalview Discussion
1

Could you tell me what java is Jalview being run with and what window manager you are using ?

Jim

J. B. Procter Jalview/enfin Barton group

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-----Original Message-----
From: “Fabian Glaser, Technion” fglaser@technion.ac.il
To: Jim Procter jprocter@compbio.dundee.ac.uk
Sent: Tue, 29 Nov 2011 6:06
Subject: Re: [Jalview-discuss] PCA custom coloring

Dear Jim,

Additionally, with the installation of the last version of Jalview on my
Ubuntu 11.10, I get a “blured” alignment when I try to slide the windows
and see different parts of the alignment.

Is there any way to overcome this problem?

Thanks,

Fabian

Fabian Glaser, PhD
Bioinformatics Knowledge Unit
The Lorry I. Lokey Interdisciplinary Center
For Life Sciences and Engineering
Technion, Haifa 32000, ISRAEL
E-mail: fglaser@technion.ac.il
Tel: +972-4-8293701

Jim Procter said the following on 28/11/11 16:42:

Hello Fabian.

On 28/11/2011 14:00, Fabian Glaser wrote:

I am new to the list, so forgive me if this a repetitive topic.

I would like to color the result of the PCA analysis but not by the
clusters selected with a tree, I would like to color selected points
on the PCA with specific colors.

Is that possible with Jalview?
It is - but only just :slight_smile: The graphical interface doesn’t really have
any controls for doing this within the program. Something that we hope
to fix in a future release.

The simplest way is to prepare an annotations file that creates a group
for each sequence in the alignment and assigns it a colour. The
annotation file has a tab-delimited structure, and its format is
described here:
http://www.jalview.org/help/html/features/annotationsFormat.html

For example, to assign colours to three sequences ‘FER1_MESCR’,
‘FER1_SPIOL’, ‘FER1_MAIZE’:

JALVIEW_ANNOTATION

SEQUENCE_GROUP\tFER1_MESCR\t0\t0\t-1\tFER1_MESCR
SEQUENCE_GROUP\tFER1_SPIOL\t0\t0\t-1\tFER1_SPIOL
SEQUENCE_GROUP\tFER1_MAIZE\t0\t0\t-1\tFER1_MAIZE
PROPERTIES\tFER1_MESCR\tidColour=red
PROPERTIES\tFER1_MAIZE\tidColour=blue
PROPERTIES\tFER1_SPIOL\tidColour=green

Note - the '\t’s need to be replaced with tab symbols!

Jim.

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