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A Transcriptome Atlas Database for Mouse Embryo
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Java Tree View

There are many tools available for visualising the results of cluster analysis. We have found JavaTreeView useful and flexible enough to allow presentation of the gene-clusters but also linking to the original data and modification to include direct import of the image data. In addition we can also provide access to pre-calculated cluster analyses via an applet version of the program which has the advantage that the programme does not need to be installed and preset behaviours for linking to external resources are already configured.

The JavaTreeView software can be obtained and installed from the SourceForge repository. It is available for Mac OSX, MS Windows and Linux. Sample usage below.

JavaTreeView - reading data.

Either generate a cluster dataset (.cdt file) or download a set from the EurExpress web-site (see analysis pages).

Start the TreeView program and read in the cluster data. You should see a dialog as shown on the left during this process.

JavaTreeView - default view

If the data has been read successfully then you should get a view as shown on the left. The cluster hierarchy will be displayed as a horizontal tree and will allow interactive selection of clusters. Here a gene cluster has been selected and the cluster members are shown on the RHS. In addition the anatomy term clusters are shown as a vertical tree above the matrix display. Use the setting controls to adjust the views to suit requirements. Here for example the pixel settings have been set to include all genes in the visible part of the tree, hence the "squashing" of the leaf nodes. To get a more open view to the gene-level reset the pixel options to say "2" so that each leaf is separated by a white line.

To get two columns on the RHS you need to make the required selections from Settings->Annotations...

JavaTreeView - gene presets

JavaTreeView - gene URL

JavaTreeView - array presets

Note the link is: <https://eurexpress.org/ee_new/databases/ anatomy/treeWindow.html?target=treeNoLinks&title=Anatomy%A0Ontology%A0Tree&emap=HEADER>

JavaTreeView - Array URL

The rows for each assay on the RH can be set to link directly to the EurExpress assay pages by modifying the Settings->URL Settings... The figures on the left show how to set up the URLs for linking both to the assay pages and for linking the anatomy terms to the anaotmy tree-view also from EurExpress.

First set the url presets to include the emage EurExpress option shown here, enabled and selected as default. Save these so that they can be re-used next time.

Next select Settings->URL Settings... and select "EurExpress" from the roww of buttons. The HEADER shownb be set to "UNIQID" as indicated by the RHS choice menu.

For the anatomy link repeat for the Array presets and URL as shown by the next two figures.

EurExpress samplle assay page

If the gene URL is set correctly then sleecting (clicking) on the gene symbol or assay ID on the RHS should produce the matching assay page from EurExpress.

EurExpress sample anatomy page

If the anatomy (array in JavaTreeView) URL is correct then selecting the anatomy ID on the top bar should produce the anatomy view from the EurExpress DB.