Interactive Visual Issues - Clusters not interactive and gene annotations not showing

brinkmanlab / IslandCompare

Pipeline for detecting and annotating genomic islands and relationships between the respective genomes

Other

4 stars 2 forks source link

Interactive Visual Issues - Clusters not interactive and gene annotations not showing #167

Closed klgray25 closed 5 years ago

klgray25 commented 5 years ago

Only some of the clusters are clickable/interactive for the visual output. Also, for some clusters, the gene annotations seem to be displaced (eg. click on the yellow cluster in the second and third genomes in the analysis): http://rcg-brinkde-1.dcr.sfu.ca/plugins/visualizations/islandcompare/show?dataset_id=2157a6833e1cf2f2&uuid=2b8d3010-78f3-11e9-9014-c7b9270b1d9e

innovate-invent commented 5 years ago

The code colors all GI's by predictor( islandpath as red, SigiHMM as blue) unless it belongs to a cluster, where it is assigned the clusters color. Not all GIs belong to a cluster.

Should we set the default to grey when "Color by simmilarity" is set?

klgray25 commented 5 years ago

Why are not all GIs assigned to a cluster? They should each have a cluster number, even if no other GIs are in the same cluster. That is what was done in the previous version.

innovate-invent commented 5 years ago

Can you try setting the minimum cluster size to 1 at workflow invocation? Are you using the dev branch or dev-merge for the original code? dev-merge has a lot of changes to the clustering code.

The title mentions gene annotations not showing, are you referring to the displaced ones?

innovate-invent commented 5 years ago

Fixed with #169 and 5e78a68a17f4d187eadcf43690ef55922a604be5