3.2 Mouse/Keyboard Functions, and Properties
     
  3.2.1 Pointer Modes
  3.2.2 Keyboard Functions
  3.2.3 Mouse Functions
  3.2.4 Embryo View Properties
3.2.5 About this PointCoud

3.2.1 Pointer Modes

Select the according button to activate the corresponding pointer mode. The currently active mode button is hightighted in green.

Name Cursor

Description

Clipping Mode
  1. Rotate/Translate the embryo
  2. Move the clipping plane if enabled
  3. Define height and offset of Expression Surfaces
Cell Selector Mode

Add or remove cells from the current Cell Selector.

Select Mode

Select the current cell which is displayed in the Cell Magnifier. The current cell is marked in gray and can also be used to execute seed cell selection (see Cell Magnifier).

3.2.2 Keyboard Functions

Button(s) Mode

Description

SPACE All Changes camera mode (revolve or fly)
A All

Toggles the display of the world axis

G All

Toggles the display of the XY grid

F All

Toggles the display of the FPS

H All Open help window
CTRL+S All Save a snapshot of the embryo view.
LEFT All Moves camera left
RIGHT All Moves camera right
UP All Moves camera up
DOWN All Moves camera down
ESC All Switch pointer mode

3.2.3 Mouse Functions

Main Mouse Controls
Button(s) Mode

Description

MIDDLE All Zooms camera to the point under the cursor
MIDDLE double click All Shows entire scene
LEFT Clipping Mode Rotates the camera
LEFT double click Clipping Mode

Aligns camera

RIGHT Clipping Mode

Translates camera

RIGHT double click Clipping Mode

Centers scene

SHIFT+LEFT Clipping Mode
  1. 3D Embryo View: Rotates the clipping plane if enabled
  2. 2D Embryo View: Move a slider of an Expression Surface to define its offset or height.
SHIFT+RIGHT Clipping Mode
  1. 3D Embryo View: Translates the clipping plane if enabled
  2. 2D Embryo View: not available
SHIFT+LEFT Cell Selector Mode Add cells to the current Cell Selector.
SHIFT+RIGHT Cell Selector Mode Remove cells form the current Cell Selector.
SHIFT+LEFT Select Mode Select the current cell which is displayed in the cell magnifier. The cell is highlighted in gray and can also be used for seed cell selection (see Cell Magnifier)

 

Secondary Mouse Controls
Button(s) Mode

Description

SHIFT + LEFT Clipping Mode  Rotates the camera
Cell Selector Mode
SHIFT + LEFT double click Clipping Mode

Aligns camera

Cell Selector Mode
SHIFT + RIGHT Clipping Mode

Translates camera

Cell Selector Mode
SHIFT + RIGHT double click Clipping Mode

Centers scene

Cell Selector Mode

3.2.4 Embryo View Properties

Press the "View Properties" button in the bottom left corner of the embryo views window to open the embryo view properties window (see also the description of the main window).

Group Property  
General Properties Select Font Shows a font select window to define the font used for the embryo view legend.
  Background Color Shows a color select window to define the used background color.
  Show Legend Enable or disable the embryo view legend.
  Show Coordinate Frame Enable or disable the coordinate frame. This option refers to the coordinate frame in the 3D embryo views (Cell View, Sphere View, and Smooth View) as well to the coordinate frame of the expression surfaces displayed in the Unrolled View..
  Projection Type Use orthographic or perspective projection..
  Clipping Plane Enables or disables the clipping plane. PointCloudXplore supports the following modes for the clipping plane in the embryo views:
  1. On Visible: Clipping plane is enabled and a ring is shown to show the position and orientation of the clipping plane
  2. On Invisible: Clipping plane is enabled but not displayed.
  3. Off: Clipping plane is disabled
  Zoom Speed Defines the speed of the zoom wheel
Sphere View Properties Radius Scale In the Sphere View each cell is represented by a sphere. These spheres are scaled according to the nuclear volume of the cell they represent. This factor can be used to define the basic radius of the sphere. 
Expression Surfaces Properties Color Scheme Defines the default coloring scheme used for expression surfaces. This option it used to define the default behaviour of expression surfaces when a  gene is selected to be displayed in a 2D physical views. Available options are:
  1. Hidden: Do not add an expression surface to the visualization when a new gene has been selected. 
  2. Single Color, Gene Color , Embryo Color: Show an expression surface using the according coloring scheme when a new gene has been selected.
Coordinate Frame
  1. Adjust to surface: Select an expression surface the coordinate frame should be adjusted to. The offset and height of the according surface are imported and assigned to the coordinate frame. The coordinate frame for the expression surfaces is only displayed in the Unrolled View. To disable the coordinate frame deselect the according check box in the general properties.
  2. Offset: Offset of the coordinate frame. The offset is the distance to the underlying 2D embryo view (Orthographic View or Unrolled View)
  3. Height: Height of the coordinate frame
  Offset Points The offset points are the base points of an expression surface. The x/y position of these points are the same as for the centers of the cells. The offset points are always colored according to the user defined basic color of the gene which the surface represents.
  1. Show offset points: Enable or disable the display of offset points.
  2. Point scale: Define the size of the offset points

3.2.5 About this PointCloud:

In the "About this PointCloud" window additional meta-data associated with the current PointCloud-file is shown. The window can be opened by clicking the according button in the lower left of the panel containing the physical views. See also the Main Window.