Saving 3D pictures

Saving 3D Pictures

This window will pop up when you try to publish a 3D graph in the clustering or classmarking module.

This window is splitted in two parts :

Save as picture : This part lets you save your 3D graph as a flat picture in a format depending on your running platform (Mac or PCs)
Save as an interactive web page : This part will generate a web page with a 3D interactive java applet displaying your current 3D view. See details below.

See a running example of the applet on our website here.

Saving as an interactive web page

You can generate a 3D java applet and its default main html page by using the "Preview" or the "Save" button at the bottom of the window. You are then free to modify this default page in your favorite html editor program. When hitting one of these two buttons, three items will be generated :

A default html page giving access to the applet. The page title will be set to the "Page Title" field, the applet title set to the "Applet Title" field, and the applet size in pixels will be set to the "Applet Size" field
A folder named "Java Classes" containing all the data needed to run the applet
A data file stored in the "Java Classes" directory with the name specified by the "Data Filename" field of the window

Using your own webpage for the 3D applet

You can discard the default html code and use your own, but you must make sure that the "Java Classes" folder is at the same level as your html page. To add the applet to your html code you must add the following lines :

To change the size of the applet, modify the WIDTH and HEIGHT attributes. If you want to keep a square ratio, set HEIGHT to WIDTH+100. The WIDTH value should be greater than 350. The parameters "HULLS", "DSCREEN", "TETA1" and "TETA2" are not mandatory.

The "HULLS" parameter when set to "YES" will check the show hulls checkbox when starting the applet. The "DSCREEN", "TETA1" and "TETA2" parameters modify the distance and angles of the viewer default values. (TETA1 and TETA2 are in radians).

The "model" value defines the dataset to be loaded into the applet.

Putting multiple 3D views in a single page

You can put multiple 3D applets in a single html file. To do so, you don't need to duplicate the "Java Classes" folder. Simply generate your 3D views in the same folder with a unique data file name (e.g. View3D1,View3D2). The models will all be saved in the "Java Classes" folder. Use the same html code as above but duplicate it as shown in the following example.

NOTE

If you check the "Include IDs" or "Include annotations" checkboxes, you will be able to click on any gene in your java applet and get its ID. If you are using the classmarker module, you will be able to add the experiment name.

NOTE

In order to correctly view the interactive applets, you need to have a java virtual machine installed on your computer. The Microsoft® virtual machine is not compatible with ArrayMiner's applets. You can download a valid java machine from Sun Microsystem® here .