Project Tree tab

The Project Tree tab is the central display of MorphoJ, which provides a graphical overview over the entire project. The following screen shot shows the elements of the user interface with the Project Tree tab selected.

The Project Tree tab displays the datasets and analyses in the project in a hierarchical tree structure. Each item is displayed by an icon corresponding to its type and a name.

In the screen shot above, the project named "flies9spp" contains a dataset named "flies" and an outline file called "outline" (this is for graphical output). In turn, the dataset "flies" has a covariance matrix named "Covariance matrix, flies, Procrustes coordinates", it was used to derive a wireframe named "flies wireframe" for use in graphical displays, it was used in a canonical variate analysis named "CVA species", and the phylogeny named "Consensus tree" was linked to it in the analysis named "Shape mapped onto Consensus tree". Additional datasets and analyses are linked to the covariance matrix and the analyses.

This structure provides an overview of the contents of the project and of the flow of the analyses.

Items in the Project Tree can be renamed or removed by invoking the pop-up menu. If the pop-up menu is called for analyses, their text output can be sent to the Results tab or their graphical output can be displayed in the Graphics tab.

If items in the Project Tree are modified (e.g. by excluding outliers, a new Procrustes fit with different alignment, etc.) the analyses that depend on the modified item are updated to reflect those changes. If many analyses depend on the modified item, the updating process can take a while (particularly if the analyses are computationally intensive, e.g. if they have permutation tests). During this process, the cursor will be shown as the operating system's 'busy cursor' (e.g. hourglass or 'spinning pizza/bagel of death'). Overall, it is good practice to check for outliers etc. at an early stage of the analysis, so that there should be relatively little need for updating of items in the Project Tree.