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 :) 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. _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
