Diagrams that show shape changes have a series of specific options to control the properties of the graph (shown in the screen shot below for a plot for a PCA for 3D data). For a general discussion on the types of graphs to visualize shape changes and the associated possibilities and problems, see Klingenberg (2013).
For explanations of the generic menu items Print, Export to SVG File and Close Panel, follow this link.
If the graph can show different shape changes, such as multiple principal components, different observations etc., the menu item Choose ... to Display can be used to switch from one to another. Using the menu item will bring up a dialog box like the following:
The list shows the available shape changes (principal components in this example). Clicking OK will change the graph to display the chosen shape change.
The scale factor is the magnification or reduction applied to the shape change that is displayed. For instance, many regressions produce shape changes that are too subtle to see and interpret easily (depending on the units used for the independent variables) and need to be amplified. In contrast, principal components are usually scaled to a length of 1.0, which corresponds to a grotesquely large shape change, which therefore needs to be reduced for display. This can be done by using Set Scale Factor, which will invoke a dialog box like this:
The current value of the scale factor is displayed in the text field (0.1 in this example). Edit this value and click OK to set a new scale factor.
The value of the scale factor can be set to a negative value to change the direction of the shape change. This is useful for some analyses, like principal components where the sign ofthe change is arbitrary, but should normally not be done for analyses like regression, where the direction of the shape change is impoprtant.
To reflect the whole diagram, select Flip Diagram. Two options will appear: Flip horizontally or Flip vertically. Flipping the diagram can be undone by fligging it again.
Graphs can be rotated by 90 degrees. When Rotate Diagram is selected in the popup menu, the options Rotate clockwise and Rotate counterclockwise appear.
This menu item appears only for graphs with 3D data, and allows the user to select which pair of coordinate axes should appear in the graph. The axes are numbered 1, 2 and 3, but may not necessarily correspond to the original coordinate axes of the raw data, depending on the options chosen for the Procrustes fit.
The different types of shape diagrams show the positions of landmarks with dots or circles. Depending on how much the diagram needs to be reduced for use in figures for publications etc., the default size of the landmark points may be too big or too small and the user may want to change their size.
The size of these points can be changed by selecting Resize Landmark Points. The following dialog box will appear:
The diameter is indicated in screen pixels and can be edited using the text field.
For wireframe and warped outline drawings, the changed point size is stored with the respective wireframe or outline drawing and will apply to any graphs produced with that wireframe or outline drawing. For lollipop graphs or transformation grids, the change will apply to any graphs of that type in the MorphoJ project and the point size is stored with the project.
The change will not apply to graphs that are already displayed in the Graphics tab; to apply the changes to those graphs, refresh them by invoking "Display Graphs" in the pop-up menu for the respective analysis or dataset in the Project Tree tab. Also, some special graphs do not share the "memory" for the diameter of points, and will appear with points that have a fixed default size each time these graphs are displayed.
This menu item appears only in wireframe graphs. If the check box is selected, the shape change is visualized with a soft wireframe, in which the straight lines of the wireframe for the starting shape (usually the average shape, etc.) is warped using the thin-plate spline interpolation for the shape change.
Selecting Change the Type of Graph invokes a secondary menu that indicates the different types of graphs that are available to visualize the shape change.
MorphoJ offers the following types of graphs for visualizing shape changes:
A lollipop graph shows the shifts of landmark positions with straight lines. Each line starts with a dot at the location of the landmark in the starting shape (often a mean shape, etc.). The length and direction of the line indicates the movement of the respective landmark.
Lollipop graphs are available both for 2D and 3D data. For 3D data, three different views can be requested by using Choose Axes To Display from the popup menu of the graph.
Transformation grids show the shape change as a deformation of a rectangular grid using the thin-plate spline. The total shape change is shown (i.e. there is no decomposition into uniform and non-uniform components, etc.).
Transformation grids are only available for 2D data. The number of horizontal and vertical grid lines can be changed via the popup menu.
Warped outline drawings are similar in that they also use the thin-plate spline, but instead of a rectangular grid, an outline drawing of the biological structure is used.
The information for the drawing must be imported into MorphoJ from a text file. For an explanation of the file format and how to import it, follow this link. Warped outline drawings are only available for 2D data.
Finally, it is possible to display the shape change as a wireframe graph. A wireframe connects selected landmarks with straight lines.
Wireframe graphs are available for 2D and 3D data. The wireframes can be defined and edited in MorphoJ by using Create or Edit Wireframe in the Preliminaries menu.
Various options for all these types of graphs for
displaying shape changes can be set through the Set Options for
Shape Graphs in the Preliminaries menu. This includes the
colors for the starting and target shapes, whether or not the
starting shape is to be shown, the default sizes of the landmark
dots, and whether the landmark numbers are to be shown (and, if
so, their color). These options apply to all graphs of a given
type that is created after setting the options.
This command (only available for graphs from 3D data) produces a dialog box that allows the user to save the 3D coordinates of the starting and taget shapes as a .DTA file for visualization as morphed 3D surfaces in the Landmark software.
The user needs to have a Landmark project with the 3D surface and the landmarks annotated on it (the same number of landmarks, and in the same order). Further information on how to use the file exported from MorphoJ to visualize shape changes with Landmark, follow this link.
Klingenberg, C. P. 2013. Visualizations in geometric morphometrics: how to read and how to make graphs showing shape changes. Hystrix 24:15–24.