PCA custom coloring

Hi all,

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?

Thanks a lot,

Fabian

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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

Hello Fabian.

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