The Main Window 3D mode


3D Objects

    The figure on the left shows a typical representation in ArrayMiner. Each 3D point represents a gene. There are four clusters in the figure (displayed in the hulls) and several unclassified genes (displayed with red crosses - note that only the Gaussian clustering model can identify unclassified genes).

    The 3D envelopes (hulls) are displayed or hidden using the "Show hulls" button in Button Panel on top of the window. They may be made translucent or opaque. Likewise, the spheres representing the genes in the cube may be shown or hidden.

 

    The 3D cube and all the data displayed inside can be easily rotated in real time into any viewing angle by simply clicking the mouse inside the cube and dragging it in the desired direction. The view can be zoomed in or out with the mouse wheel. Note that while the gene-spheres and transparent hulls are extremely convenient for assessing the relationships among the data, they are somewhat slower to manipulate this way (on a PC, see also the Graphic Image Depth option in the Window menu).

    You can also change the postion of the center of the 3D cube by holding the Shift key while draging the graph. To change the perspective, drag the figure while holding the Alt key. (1.0 correction is the standard projection and 0.0 is the isometric projection without any perspective).

    To allow for a convenient (i.e., fast) adjustment of the viewing angle, 3D the representation is changed during rotation to a less resource-demanding mode. However, on sufficiently powerful computers, showing the desired representation even during rotations is a must. It is achieved by simultaneously pressing the Shift and Alt keys when starting to drag the mouse.

 
Selected Gene in the 3D View
   The selected gene is drawn in a target. To select a gene, simply right click on it and choose "Select Item" in the popup menu. You can also use the Search facility to select a gene.

    You can hide a cluster by moving the cluster to its hull (if the hulls are visible) or to a gene and hitting the "X" key. Note that the "A" key will set all the cluster to the visible state and the "I" key will invert the visible selection of the clusters.
 
Objects in the 3D View
     

Contextual Menus

  • Background contextual menu :
    • The "Show all" option turn all the clusters to the visible state.(You can also use the "A" shortcut)
    • The "Invert selection" option invert the visible state of all clusters
    • The "Copy 3D cube position" option lets you copy the currently parameter of the 3D view
    • The "Paste 3D cube position" option lets you paste a previously copied position of the 3D view
    • The "Reset 3D cube position" option lets you reset all the parameters of the view to defaults
  • Hull contextual menu :
    • The "Hide group" option will hide the gene's cluster
    • The "Show all" option turn all the clusters to the visible state.(You can also use the "A" shortcut)
    • The "Invert selection" option invert the visible state of all clusters
    • The "Copy 3D cube position" option lets you copy the currently parameter of the 3D view
    • The "Paste 3D cube position" option lets you paste a previously copied position of the 3D view
    • The "Reset 3D cube position" option lets you reset all the parameters of the view to defaults
  • Gene contextual menu :
    • The "Select item" option will select the gene
    • The "Hide group" option will hide the gene's cluster
    • The "Best point of view from this cluster" option shows the selected cluster in the most significant axes
    • The "Show cluster in closest clusters" option opens the closest cluster window with the currently selected cluster
    • The "Show all" option turn all the clusters to the visible state.(You can also use the "A" shortcut)
    • The "Invert selection" option invert the visible state of all clusters
    • The "Copy 3D cube position" option lets you copy the currently parameter of the 3D view
    • The "Paste 3D cube position" option lets you paste a previously copied position of the 3D view
    • The "Reset 3D cube position" option lets you reset all the parameters of the view to defaults