I just figured out if I remove 'key' => 'ensembl' from the web_data, the colours show correctly.<br>This is probably that ensembl genes colour_key works differently.<br><br>Thanks.<br><br><br>//Ha<br>
<br><br><div class="gmail_quote">On Fri, Nov 5, 2010 at 2:15 PM, Ha X. Dang <span dir="ltr"><<a href="mailto:dxha@vt.edu">dxha@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Ensemblers,<br><br>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:<br>
<br>analysis_description.web_data = {'colour_key' => 'geneid_gene',
'caption' => 'Genes','label_key' => '[text_label]
[display_label]','name' => 'Genes','default' => {'MultiTop' =>
'gene_label','<div>contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label','cytoview' => 'gene_label'},'key' => 'ensembl'}<br>
<br>geneid_gene, gene_wise, etc. colour keys were already configured in COLOUR.ini file in [gene] section.<br><br>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.<br>
<br>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:<br><br>$gene->{my_config}{_tree_info}{nodes}{transcript_core_ensembl}{data}{colour_key}?<br>
<br>I think there is some bug with this module.<br><br>Thanks a lot.<br><font color="#888888"><font color="#888888"><br><br>//Ha</font></font></div>
</blockquote></div><br>