[ensembl-dev] Gene/transcript colour_key not loaded properly

[Will Spooner]

Hi Ha,

The module to look at is;
  ensembl-draw/modules/Bio/EnsEMBL/GlyphSet_transcript.pm

You will notice a set of render_* methods; e.g. 'MultiTop' => 'gene_label' will cause the render_gene_label method to be called from the MultiTop view. Each render method specifies it's own approach to setting the feature colours.

Best,

Will

On 5 Nov 2010, at 18:15, Ha X. Dang wrote:

> Hi Ensemblers,
> 
> I'm using Ensembl v56 and I have a genes predicted by several programs and want to color them differently in region view, so I add colour_key to the web_data field of the analysis corresponding to the gene predictor, eg. for geneid I have:
> 
> analysis_description.web_data = {'colour_key' => 'geneid_gene', 'caption' => 'Genes','label_key' => '[text_label] [display_label]','name' => 'Genes','default' => {'MultiTop' => 'gene_label','
> contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label','cytoview' => 'gene_label'},'key' => 'ensembl'}
> 
> geneid_gene, gene_wise, etc. colour keys were already configured in COLOUR.ini file in [gene] section.
> 
> Howerver, it doesn't seem to load the colour_key correctly for the gene object. I dumped the data and saw that for all genes/transcripts, the colour_key is always the same (eg. 'genewise_gene') and that made all genes/transcripts to have the same display color.
> 
> Could someone have any idea on how this happens or point me to the module that load the web_data (colour_key) for gene/transcript object? Specifically, what is the module that loads:
> 
> $gene->{my_config}{_tree_info}{nodes}{transcript_core_ensembl}{data}{colour_key}?
> 
> I think there is some bug with this module.
> 
> Thanks a lot.
> 
> 
> //Ha
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--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com