Graphia Pro:Manual

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This is a detailed functional look at all elements within Graphia Pro. If you are looking for a more user-friendly guide to getting started with Graphia Pro, try Graphia Pro:Tutorials

Contents

 Hotkeys

Navigate

Hotkey Action
SHIFT+LEFT CLICK Centre Graph on a Specific Node
R Rotate Graph

Open Controls

Hotkey Action
CTRL+C Open Class Viewer
SHIFT+S Open Graph Statistics

Select

Hotkey Action
SHIFT+Drag Left button Select Nodes
SHIFT+ALT+Drag Left button Select Additional Nodes Without Unselecting Selected
CTRL+ALT+S Select Nodes Within The Same Class
CTRL+N Select Neighbours
CTRL+ALT+C Select Children
CTRL+ALT+P Select Parents
CTRL+R Reverse Selection
CTRL+U Unhide All Nodes
CTRL+L Show Selected Node Names

Node Size

Hotkey Action
SHIFT+< Decrease Size of Selected Nodes
SHIFT+> Increase Size of Selected Nodes

Hide

Hotkey Action
CTRL+H Hide Selection
CTRL+SHIFT+H Hide Unselected
CTRL+ALT+SHIFT+H Hide All Node Names

Other

Hotkey Action
CTRL+Z Undo Node Dragging On Selection (2D only)
ALT+P Save Preferences

 Navigation

Using the 3D Interface

Visualization of networks in 3 dimensions provides a fast and powerful interface to enable understanding of the often-complex relationships between the entities represented in a graph.  

To interact with 3D graphs: 

  • Left mouse button for rotation of the current view.  
  • Middle mouse button for sideways movement (translation) of the current view.  
  • Right mouse button for zoom in/out.  
  • Holding down Shift + Click the left mouse button on a node selects it and makes it the centre of the graph.  
  • Holding down Shift while dragging the left mouse button is used to select multiple nodes in the graph.  
  • Holding down Shift + Alt while dragging the left mouse button is used to select more nodes in the graph, without deselecting the previous ones. 

These commands are also available under the 3D menu, the Navigation Wizard and the Navigation tool bar (Figure 1). Please see the Tool Bars section in this manual.

Using the 2D Interface

To interact with 2D graphs:  

  • Left mouse button for moving around the current view (translation).  
  • Right mouse button for zoom in/out.  
  • Holding down Alt + Click the left mouse button on a node selects it and makes it the centre of the graph (when at default view only).  
  • Holding down Shift while dragging the left mouse button is used to select nodes in the graph.  
  • Holding down Shift + Alt while dragging the left mouse button is used to select more nodes in the graph, without deselecting the previous ones.  
  • Ctrl + Z to undo last action, Ctrl + Y to redo last action. 

These commands are also available under the 2D menu bar, the Navigation Wizard and the Navigation tool bar (please see the Navigation Wizard and the Tool Bars sections in this manual).   

Main Window

 The Menu Bar

Menubar.png

File

  •     Open: Opens a graph file. Supported file types are: blast, owl, expression, graphml, mepn, layout, sif, tgf, txt, matrix, xml (Ondex xml format, www.ondex.org). (CTRL+O)  
  •     Open Recent: Opens a previously opened graph file from a history of a maximum of 10 previously opened files.  
  •     Save Graph As…:  Opens the Save dialog and saves the whole graph. The supported saving file types are: layout, tgf. (CTRL+S)  
  •     Save Graph Selection As…: Opens the Save dialog and saves the currently selected parts of the graph. (CTRL+SHIFT+S)  
  •     Save Visible Graph As…:  Opens the Save dialog and saves the currently visible graph. (CTRL+ALT+V)  
  •     Import: Provides access to the Import sub-menu (see below for details).  
    •     Class Sets…: Imports Class Sets for the currently loaded graph. The user is guided with relevant dialogues so as to choose Class Sets to parse from the imported file along with the Node Identifier Parsing Options. The supported file types as of Version 2.0 are: classsets  
    •     Network from Public Database…:  Query the Pathway Commons resource and import BioPAX pathway networks  
  •     Export: Provides access to the Export sub-menu (see below for details).  
    •     Class Sets As File…:  Provides access to the Class Sets As File secondary sub-menu (see below for details).  
      •     From Graph…:  Opens the Save dialog and exports Class Sets from the whole graph. The supported saving file types as of Version 2.0 are: classsets  
      •     From Graph Selection…:  Opens the Save dialog and exports Class Sets from the currently selected graph.  
      •     From Visible Graph…:  Opens the Save dialog and exports Class Sets from the currently visible graph.  
    •     SBGN File…:  Converts a mEPN diagram to SBGN format and exports to file..  
  •     Print Page Setup:  Opens the Print Page Setup dialog for setting printing selections. (CTRL+SHIFT+P)  
  •     Print Graph:  Opens the Print dialog and prints the graph. (CTRL+P)  
  •     Exit:  Exits the application. A confirmation dialog will be presented in case a file is already loaded.  

Edit

  •     Selection: Provides access to the Selection sub-menu (see below for details).  
  •     Select All: Selects all nodes in the currently loaded graph. (CTRL+A)  
  •     Select Neighbours: Selects the immediate neighbours, inputs (parents) and outputs (children), of the currently selected nodes. (CTRL+N)  
  •     Select All Neighbours: Selects all the neighbouring (parents and children) nodes in relation to the current selection. (CTRL+SHIFT +N)  
  •     Select Parents: Selects the immediate input (parent) nodes in relation to the current selection. (CTRL+ALT+P)  
  •     Select All Parents: Selects all the parent nodes in relation to the current selection. (CTRL+ALT+SHIFT+P)  
  •     Select Children: Selects the immediate output (children) nodes in relation to the current selection. (CTRL+ALT+C)  
  •     Select All Children: Selects all the child nodes in relation to the current selection. (CTRL+ALT+SHIFT+C)  
  •     Select Nodes Within the Same Class:  Selects all the nodes that are part of the same selected class. (CTRL+ALT+S)  
  •     Reverse Selection: Reverses the current nodes selection i.e. unselects currently selected nodes and selects all the remaining nodes. (CTRL+R)  
  •     Deselect All: Deselects all nodes (selection reset). (CTRL+ALT+A)  
  • Undo Node Dragging  
    • On Selection: Undoes node dragging on currently selected nodes (2D only). (CTRL+Z)  
  • Redo Node Dragging    
    • On Selection: Redoes (restores) node dragging on currently selected nodes (2D only). (CTRL+Y)  
  • Delete Selection: Deletes all currently selected nodes. (CTRL+ALT+D) •  Delete Hidden: Deletes all currently hidden nodes.    
  • Delete Unselected: Deletes all currently unselected nodes. (CTRL+ALT+SHIFT+D)  
  • Undo Last Delete: Undoes (restores) the last deleted nodes. (CTRL+ALT+Z)  
  • Undelete All Nodes: Undeletes all nodes. (CTRL+ALT+SHIFT+Z)  
  • Collapse Nodes By Class: Collapses (unifies) all the nodes with group nodes representing their class. The size of the collapsed group node is proportional to the number of the original nodes associated with that class. (CTRL+ALT+SHIFT+G)  If size of collapsed nodes is too big i.e. they overlap, the user can reduce them in size manually.  
  • Collapse Selection: Collapses (unifies) all the currently selected nodes into a group node. (CTRL+ALT+G)  
  • Perform Complete Grouping:  Performs complete grouping for the whole graph. (CTRL+ALT+C)  
  • UnCollapse Selected Groups:  Uncollapses (de-unifies) all the selected collapsed group nodes. (CTRL+ALT+SHIFT+S)  
  • UnCollapse All Groups: Uncollapses (de-unifies) all the collapsed group nodes. (CTRL+ALT+SHIFT+U)  
  • Filter Nodes By Edges: Opens the Filter Nodes By Edges dialogue, in which the user can interactively filter out nodes based on their number of edges, hiding nodes with a number of edges below a selected threshold. Note that the edges filter may end up with nodes that seem to have fewer edges attached to them than the currently selected threshold but in reality some of their attached edges may be already hidden from other nodes that were previously filtered out. (CTRL+W)  
  • Filter Edges By Weight: Opens the Filter Edges By Weight dialogue, in which the user can interactively filter out edges, based on their representative weight, in a graph with weighted edges e.g. expression graphs. Edges below a selected weight threshold are filtered out. If the option Also Hide/Unhide Nodes is selected, nodes that are left with no edges are also filtered out. Note that this option is NOT available for input files that do not provide weight information. (CTRL+ALT+W)  

View

  •      Toggle 2D/3D: Toggle 2D or 3D display mode.  
  •      Hide Selection: Hides (but does not delete) selected nodes. (CTRL+H)  
  •      Hide Unselected: Hides (but does not delete) unselected nodes. (CTRL+ SHIFT+H)  
  •      Unhide All Nodes: Unhides all nodes. (CTRL+U)  
  •      Show All Node Names: Shows all node names. (CTRL+SHIFT+L)  
  •      Show Selected Node Names: Shows all selected node names. (CTRL+L) 
  •      Show All Edge Names: Shows all node names. (CTRL+SHIFT+K)  
  •      Show Selected Nodes Edge Names:  Shows all selected node names. (CTRL+K)  
  •      Hide All Node Names: Hides all node names. (CTRL+ALT+SHIFT+H)  
  •      Hide Selected Node Names:   Hides all selected node names. (CTRL+ALT+H)  
  •      Hide All Edge Names: Hides all node names. (CTRL+ALT+SHIFT+J)  
  •      Hide Selected Nodes Edge Names:  Hides all selected node names. (CTRL+ALT+J) 
  •      Show Classes Legend: Opens the Classes Legend dialogue, which provides the user with a reference of all node classes and their associated colours. (CTRL+ALT+L)

Search

  •      Find By Name: Opens the Find By Name dialogue, in which a user can interactively search for nodes, based on a search term. Matching nodes are selected in the graph.. If the search term is not found in the graph, a pop-up dialogue is displayed. (CTRL+F)  
  •      Find By Class: Opens the Find By Class dialogue where the user can interactively search for a given class. A Class is chosen from a drop-down listing all of the Classes in the graph. Matching nodes are selected in the graph. If no classes are present, the ‘No Class’ selection is the only option available in the class selection drop down menu. (CTRL+SHIFT+F)  
  •      Find By Multiple Classes: Opens the Find By Multiple Classes dialogue, in which the user can interactively search for multiple classes. The dialogue contains a list of Classes present in the graph; to search for a class, check the associated checkbox. The ‘Select/Deselect All’ dialog buttonallows the user to select or deselect all classes. If no classes are available, the ‘No Class’ selection is the only one available in the multiple classes selection table. Matching node(s) are selected in the graph. (CTRL+ALT+SHIFT+F)

Simulation

  •      Signalling Petri Net (SPN) Simulation: Opens the SPN Simulation dialogue, in which a user can enter the parameters for the Signalling Petri Net simulation algorithm.    
  •      SPN Simulation Options:  
    •      Assign a number of time blocks. A time block is the time frame in which a transition is fired exactly once.  
    •      Assign a number of runs. This is the number of runs over which the simulation is repeated.  
    •      Check the checkbox labelled Calculate Error if error calculation is required  
    •      In Choose SPN Stochastic Distribution, select the type of probabilistic distribution of values that is required. Options are:  
      •      Uniform    
      •      Standard Normal Distribution.  
      •      Deterministic Process o In Choose SPN Transition Type, select a transition type:    
      •      Consumptive Transitions – tokens are consumed from input places and placed at the end of output arcs.  
      •      Original Transitions    
      •      After processing of the SPN simulation algorithm has finished, the user can choose to save the simulation results to a file for further inspection. (ALT+S)    
  •      Load Simulation Data: Loads a saved simulation results file. The supported file types are: .spn, .txt. (ALT+L) •  Simulation Animation Control: Opens the Simulation Animation Control dialogue in which the user can select options to control visual aspects of the animation of the simulation algorithm results. GPU Computing is used for the real-time animation visualization (enabled by default if available). (ALT+A)  
  •      Node Animation – options for which nodes are to be animated and the type of animated transition that takes place between node states.  
  •      Timing  
    •      Time Blocks per Second – controls the speed of animation  
    •      Start from TimeBlock – the time block from which the animation begins  
  •      Size Transition – options to control proportional size of nodes.  
  •      Colour Palette Spectrum Transition – options to control changes in colour as node token values change.  

Help

  •      Navigation Wizard: Opens the Navigation Wizard dialogue, which provides a quick reference guide to interacting with both 2D and 3D graphs as well as direct links to the Graphia Pro website. (SHIFT+N)  
  •      Tip Of The Day: Opens the Tip Of The Day dialogue, providing handy tips for various functionalities of the application. (SHIFT+T)  
  •      Licenses: Opens the Licenses dialogue, providing detailed information on the software license. (SHIFT+L)  
  •      OpenGL Driver Caps: Opens the OpenGL Driver Capabilities dialog, providing detailed information about the computer’s OpenGL graphics hardware and its OpenGL extensions and GLSL support. (SHIFT+G)  
  •      OpenCL Driver Caps: Opens the OpenCL Driver Capabilities dialog, providing detailed information for the computer’s OpenCL GPU Computing hardware and its OpenCL extensions and support. (SHIFT+C)  
  •      Java Platform Caps: Opens the Java Platform Capabilities dialog, providing detailed information of the computer’s Java Platform and environment.  (SHIFT+J)  
  •      Check For Updates: Checks for application updates in theGraphia Pro website. Relevant messages will inform the user regarding the availability of a newer update of the application. (SHIFT+U)  
  •      About: Opens the About dialog, providing author credits, copyright and support information. (SHIFT+A)  

2D

  •      Toggle AutoRotate/Profile: Turns on/off 2D auto-rotation and displays the mean framerate speed per second (FPS), providing a measure of performance. Unless Graph Properties -> Rendering -> VSynch is turned on (please refer to Reference 1), the higher the number reported, the better.  
  •      Toggle ScreenSaver  ® : Turns on/off the 2D ScreenSaver, showcasing performance and presenting the application logo to users through real-time graphical effects. •  Translation Mode: Enables a 2D navigation mode where the left mouse button is used for moving the graph around and the right mouse button for zooming in/out. •  Zoom Mode: Enables a 2D navigation mode where the left mouse button is used for zooming in/out and the right mouse button for moving the graph around. •  Recenter View: Recenters the view for the 2D graph. •  Render Graph Image To File As…: Opens the Render Graph Image to File As dialogue and renders the current view of the 2D graph to an image file (either .png or .jpg) in a user-selected folder. •  Render High Res Graph     Image To File As…: Opens the Render High Res Graph Image to File As dialogue and renders the current view of the 2D graph to a high resolution image file (either .png or .jpg) in a user-selected folder. The quality of the high-resolution image file can be adjusted with the Graph Properties ! Rendering ! Scale value (please refer to Reference 1).  

3D

  •      Toggle AutoRotate/Profile: Turns on/off 3D graph auto-rotation and calculates the mean frame rate speed per second (FPS), providing a measure of performance. Unless Graph Properties ! Rendering ! VSynch is turned on (please refer to Reference 1), the higher the number reported, the better.  
  •      Toggle Pulsation/Morphing: Turns on/off a 3D graph pulsation/morphing effect. 
  • Rotation Mode: Enables a 3D navigation mode where the left mouse button is used for rotating the graph and the right mouse button for zooming in/out.  
  • Selection Mode: Enables a 3D navigation mode where the left mouse button is used for selecting nodes in the graph and the right mouse button for zooming in/out. Selection can always be initiated by having the SHIFT key pressed down in any other navigation mode. 
  • Translation Mode: Enables a 3D navigation mode where both mouse buttons are used for moving the graph around.  
  • Zoom Mode: Enables 3D navigation mode where both mouse buttons are used for zooming in/out the graph. 
  • Recenter View: Recenters the view for the 3D graph. •  Render Graph     Image To File As…: Opens the Render Graph Image to File As dialog and renders the current view of the 3D graph to an image file (either .png or .jpg) in a user-selected folder.  
  • Render High Res Graph Image To File As…: Opens the Render High Res Graph Image to File As dialog and renders the current view of the 3D graph to a high resolution image file (either .png or .jpg) in a user-selected folder. The quality of the high-resolution image file can be adjusted with the Graph Properties ! Rendering ! Scale value (please refer to Reference 1). 

Graph Properties Tabs

The Graph Properties dialogue consists of a series of tabbed panes, which provide access to the options available in the Graphia Pro application, divided into 10 distinct groups. All of the tabs are presented in the picture below (Graph Properties dialogue)

A menu is available at the top menu of Graphia Pro to allow rapid access to tabs

GraphPropertiesMenu.png

Graph Properties dialog General tab

General

Background Colour Options

Background Colour Options: Settings for Background/Selection/Plot Background/Plot Grid Lines

  • Background colour: When clicked, the user can define the background colour for the graph through the Color Chooser dialog (below):

  Through this dialogue, the user can define colours for the 2D/3D mode background, node selection (the colour node(s) have when selected) and the plot background in Expression, Class Viewers and the Popup Overlay Plot. Please refer to the Expression and Class Viewers sections of this manual for details.   

General Graph Options
  • Disable Nodes Rendering For Graph: (default off) checkbox provides the option to turn off the visualization of nodes. This can help when rendering very large graphs (and/or for machines with lower specs graphics hardware) and can also help in the visualization of graph topology.  
  • Disable Edges Rendering For Graph: (useful for very large graphs, default off) checkbox provides an optimisation path for viewing very large graphs (and/or for machines with lower specs graphics hardware) by not rendering graph edges.
  • Directional Edges: (2D graphs only) (default off) checkbox adds arrowheads to edges, thereby showing the directionality of the edge. This option is available for 2D graph view representation only.  It show also be noted that there is a considerable overhead in rendering arrowheads so this may affect rendering speeds when used with large graphs. For expression and matrix derived graphs, this option is disabled automatically as there is no directionality information for these graphs.  
  • Show Edges when dragging nodes: (2D graphs only) (default on) checkbox provides edge rendering while node dragging (2D graph view representation only). Note that if you experience poor performance while dragging nodes, turning this option off may improve performance. The application automatically chooses the best option for the user at first program launch, using the OpenGL GPU Computing framework.  
  • yEd-style rendering for graphml files: (default on) checkbox provides yEd-style rendering for .graphml files that include positional data, bypassing the built-in layout positioning algorithm. Enabled only when a graphml file has been loaded.
  • yEd-style Component Containers Rendering for Graphml files: (default on) checkbox provides yEd-style rendering for .graphml files that include component containers. Enabled only when a graphml file has been loaded.
General Options
  • Use application’s install directory for Render Image To File screenshots (default off) checkbox provides default selection behaviour for saving the Render Image To File screenshot in the folder in which the application is installed, instead of the default location, i.e. the directory where the current graph was loaded from.  
  • Use application’s install directory for MCL temporary file (in MCL folder) (default off) checkbox provides default selection behaviour for saving the MCL temporary File in the MCL folder instead of the default location, i.e. the temporary folder set from the underlying Operating System. This way the MCL file can be more easily found and opened for further examination.  
  • Show Graph Properties ToolBar (default on) checkbox enables/disables the Graph Properties tool bar on the main application view (please read more about all available tool bars in The Tool Bars section).  
  • Show Popup Overlay Plot (default on) checkbox enables/disables the Popup Overlay Plot on the main application view.  
  • Show Navigation Wizard On Startup (default on) checkbox displays the Navigation Wizard dialogue when the application starts. The Navigation Wizard provides detailed information of the navigation controls of 2D/3D views.  
  • Show Layout Iterations while loading graph (only when Layout -> Tiled Layout option is disabled) (default off) checkbox provides functionality of displaying the stages of the layout process while the graph is being loaded. Please note that it will work only if the Layout ! Tiled Layout checkbox in the Layout tabbed options pane window is checked as well.  
  • Validate XML files when loading (default off) checkbox provides XML validation as an extra level of integrity checking for parsing of XML-based files (.graphml files) at a small cost of loading speed. Any XML error messages will be displayed to the user within an error message dialog.  
  • Show Navigation ToolBar (default on) checkbox enables/disables the Navigation tool bar on the main application view (please read more about all available tool bars in The Tool Bars section).
  • Collapse Nodes By Volume (default off) checkbox provides node collapsing by volume, instead of the default behaviour of collapsing by node radius (see Edit menu for details of collapse node function).  
  • Confirm Preferences Save On Exit (default on) checkbox confirms if the preferences should be saved whenever the application is exited.

Layout Tab

Layout Graph Properties
Algorithm

(default Fruchterman-Rheingold) selects the algorithm used to place the nodes of the graph.  

  • Fruchterman-Rheingold is the traditional approach
  • FMMM (Fast Multi-pole Multi-level Method) is an alternative algorithm that works well on large graphs in particular. The implementation used in Graphia Pro is a port of the algorithm available from the C++ based Open Graph Drawing Framework library.  
  • Circle is a simple and fast algorithm that distributes the nodes in a circle
  • Always Ask will prompt the user on loading a model asking which layout algorithm to use

Minimum Component Size (default value 3) textbox provides control over the minimum size allowed for components. Graph components with fewer nodes than the number selected will be removed from the graph

FMMM Options

Desired Edge Length (default value 20) indicates to the algorithm a target edge length to strive for.

  • Force Model (default value Fruchterman-Rheingold) selects the force model used to compute the final layout. The two options are Fruchterman-Rheingold and Eades, the former is less accurate but faster to compute, while the latter is the opposite.
  • Quality vs. Speed (default value Medium Quality Medium Speed) indicates the trade-off employed between layout quality with respect to the time taken to compute the layout. This setting is useful for particularly large graphs where the time to compute the layout may be prohibitively long.
  • Stop Criterion (default value Force Threshold and Fixed Iterations) FMMM is an iterative algorithm meaning it performs the same operation repeatedly in order to converge on a final layout. The implication here is that at some point the algorithm must decide when to stop iterating. This setting indicates the criteria with which the algorithm will decide when to cease. Choosing Force Threshold will stop when the forces between nodes drop below an automatically defined threshold. On the other hand Fixed Iterations will stop after an automatically predefined number of iterations. The default value is to stop on whichever criterion occurs first.
  • Iteration Level Factor (default value 10) The FMMM algorithm is a so-called “multi-level” graph algorithm in that it performs its operations on a selection of coarsened representations of the original graph. This approach is taken in order to improve the overall performance of the process. The Iteration Level Factor setting determines how the number of iterations employed varies between multilevel representations of the graph.
Fruchterman-Rheingold options
  • Use Edge Weights For Layout (default on) checkbox provides functionality for using the edge weight between two nodes as a bias when processing the layout algorithm.
  • Tiled Layout (default on) checkbox provides selection behaviour for the layout algorithm to place all components of the graph in a tiled presentation. If set to off, the graph will be presented with an organic layout space distribution. Please note that the General ! Show Layout Iterations while loading graph option will only work if this option is also enabled.
  • Start Temperature (default value 100.0) textbox provides functionality for selecting the starting temperature of the layout process. Generally the default value does not need to be changed.
  • Number Of Layout Iterations (default value 100) provides control over the number of times the layout algorithm will iterate through the layout process. The default setting should allow layout process to reach a stable equilibrium. Increasing the number will increase the time taken for the overall layout process. Generally the default value needs not to be changed.
  • K-Value Modifier (default value 1.0) textbox provides functionality for selecting the K-Value modifier of the layout process, which controls the node repulsion force during layout. Generally the default value needs not to be changed.  
  • Burst Layout Iterations (default value 20) textbox provides control over the number of times the layout algorithm will iterate through the layout process when an existing graph is re-laid out (please refer to General Tool Bar Icon 10 for usage)  
Rendering Graph Properties

Rendering Tab

General OpenGL Rendering Options
  • 3D Nodes Tessellation (default value 10 or 15) slider bar provides control over the rendering quality of the 3D nodes. Higher values infer greater detail in rendering, at a cost of reduced speed and greater video memory usage.  
  • Show Nodes When Navigating (default on) checkbox provides optimization for viewing large 2D and 3D graphs (and/or for machines with lower specs graphics hardware) to not render the nodes when the user is interacting/navigating within the graph.
  • High Res Graph Image Scale (default value 5) slider bar sets the scale factor used when the graph is saved as a high resolution image to a file (up to 20x), when the Render High Res Graph Image To File As… option is selected (please refer to Menu -> 2D and Menu -> 3D). For most purposes, the default value provides a publication quality image. High values will lead to very large files.  Node legends may be lost during the rendering of a high resolution image due to its fragmentation during the saving process.    
  • Enable Keyboard Shortcuts (default off) checkbox provides support for controlling the 2D and 3D OpenGL renderers directly through keyboard shortcuts. Please refer to the Advanced Keyboard Rendering Control section of this manual for all the available keys.  
3D Lighting, Fog & Motion Blur Options
  • Light X/Y/Z (default values 0/4/1) slider bars provide control of the values of the 3D lighting vector, used for the various OpenGL lighting shading models, for all of the 3D nodes. Changes in these values will interact with each 3D node’s normal vector, so as to provide a different angle of lighting.  
  • Depth Fog (Per-Pixel with Advanced Shaders) (default on) checkbox enables fog rendering, thus emulating a sense of depth fog as the graph is zoomed in and out.
  • Motion Blur (default off) checkbox enables Per-Frame motion blur rendering.
  • Motion Blur Size (default value 50) slider bar provides control of the amount of motion blur active within the scene.
3D Node Material and Shading Options

Settings for the material and shading used to realistically render nodes in 3D 

  • Specular (default on) checkbox enables specular lighting and shading, for the various OpenGL lighting and shading models, for all of the 3D nodes. Note that this option will automatically enable/disable all the Advanced (PerPixel) GLSL Shaders (if available).  
  • Gouraud (Per-Vertex) Smooth Shading (default on) checkbox enables the original legacy fixed pipeline smooth shading for the OpenGL lighting and shading model for all of the 3D nodes. Note that this option is available by default when all the Advanced (Per-Pixel) GLSL Shaders are turned off, so as to provide a crude lighting shading model with the original legacy OpenGL fixed pipeline, else one of the Advanced (Per-Pixel) GLSL Shaders is used instead (if available).  
  • Spherical Mapping (default on) checkbox enables spherical mapping texture coordinates support, for all of the 3D nodes. It is also used in conjunction with the Show 3D Environment Mapping option.
  • Shininess (default value 25) slider bar provides selection of the shininess value, for the various OpenGL lighting/shading models, for all the 3D nodes.
  • AntiAlias Shading (For Toon, Gooch, Brick and Hatching Advanced Shaders) (default on) checkbox provides anti-aliasing support for the aforementioned Advanced Shaders. Note that the underlying OpenGL hardware must provide support for the Advanced (Per-Pixel) GLSL Shaders for this option to be available; else this checkbox is automatically disabled.  
  • Animated Shading (default on) checkbox provides animation support for the aforementioned Advanced Shaders. Note that the underlying OpenGL hardware must provide support for the Advanced (Per-Pixel) GLSL Shaders for this option to be available; else this checkbox is automatically disabled.  
  • Alternate Shader Rendering (default on) checkbox provides a more precise Advanced Shader diffuse rendering pipeline. For a number of effects it also provides an alternate Advanced Shader rendering pipeline. Note that the underlying OpenGL hardware must provide support for the Advanced (Per-Pixel) GLSL Shaders for this option to be available; else this checkbox is automatically disabled.  
  • Node Surface Image Texture (default off) checkbox provides the option of using a surface image texture to render all the nodes. The default image is the application’s icon, with more selections available in the drop-down menu. The user can also select an image file by clicking the Load button (accepted formats are .png, .jpg and .gif images). The Clear button clears the selection and reverts to the default image (the application’s logo). 

MCL (Markov Clustering Algorithm) Tab

MCL graph properties tab
  • Inflation (default value 3.0) slider bar provides control over the MCL algorithm, by adjusting its inflation parameter. Inflation affects the granularity of the resulting clustering. Lower the inflation value to obtain coarser clusters and increase it for more granular clusters. This is the single most important parameter to the MCL algorithm.
  • Pre Inflation (default value 3.0) slider bar provides control over the MCL algorithm by adjusting its pre-inflation parameter. This option instructs MCL to start with an inflation step. This has the effect of skewing the weights in the graph such that heavier edges gain importance, resulting in more granular clusters. This option will likely have little effect when clustering graphs derived from expressions data using the Pearson correlation.
  • Scheme (default value 6) slider bar provides control over the MCL algorithm, by adjusting its scheme parameter. This affects the computational resources available to MCL. A lower setting allows fewer resources, and may speed up MCL when clustering very large graphs. Users should generally not need to change this option.  
  • Smallest Cluster Allowed (default value 3) textbox provides control over the MCL algorithm, by post-processing its result.  Only those clusters above the threshold number of nodes specified by this value will be assigned to a Class; nodes in clusters smaller the than the assigned value will be listed as having No Class in the output file.
  • Assign Random Cluster Colours (default off) checkbox provides functionality for assigning random colours to node clusters (classes), instead of using the default behaviour of assigning distinct pre-defined colours chosen from a modulo cyclic colour pool group.
  • MCL Advanced Options (default empty) textbox provides advanced control over the MCL algorithm for experimental and/or undocumented MCL features. For expert users only, otherwise please leave empty.
  • Cluster Graph Using MCL button will run the MCL clustering algorithm from within the Graph properties window

Simulation Tab

Signaling Petri Net (SPN) Simulation Options
  • Save SPN Results (default off) checkbox enables saving the SPN stochastic flow simulation results in a text file (default extension .spn). The name of the file is automatically generated, based on the number of Time Blocks, Runs and the name of the loaded graph.
    • The user can select the output folder with the Save SPN Results At Folder button.  
    • The Clear button clears the last folder selection.  
    • Default (an empty selection) folder is the program’s current running folder.  
  • Automatically save SPN Results to pre-chosen folder (default off) checkbox enables automatic SPN saving, after the SPN stochastic flow simulation is finished, in the folder selected with the option above.
  • Use SPN Animated Transitions Shading (3D Graphs Only) checkbox enables additional graphic effects during SPN Animations

Search Tab

  • The user can choose one of the pre-defined search site links from the drop-down menu to be used when searching for a node name on the web (the default search engine for words is Google). The actual link used is shown in the text box underneath the drop-down menu. Note that the web search for a node name is performed when the user clicks on a particular node on the graph while having CTRL pressed down (CTRL+left mouse button click); the system default web browser opens and runs the search.
  •  The user can define a custom search link to perform a web search, if a search engine or gene database not provided in the the pre-set searches is required. 

Nodes Tab

Node Graph properties Tab
Node Identifier
  • Node Identifier textbox displays the current selected node ID (name). It also provides functionality to rename the current node ID (name). Note that the Node Identifier textbox is only enabled for a single node selection. When selecting more than one node, the textbox is automatically disabled.
2D/3D Node Shape, Transparency and Colour (Overrides Class Colours)
  • 2D Shape (default CIRCLE) drop-down menu provides a choice of 2D shapes for the currently selected node(s) to be rendered as (2D mode only).  
  • 3D Shape (default SPHERE) pull down menu provides a choice of 3D shapes for the currently selected node(s) to be rendered as (3D mode only).
  • Transparency (default on) checkbox provides the option to render the currently selected node(s) with a chosen transparency value. When enabled, the user can use the Alpha slider bar to choose a transparency setting (0.0 - 1.0 range, default 0.5, node(s) appear semi-transparent).  
  • Color button enables the user to override the default Class colour for the selected node(s). A colour is selected through the Colour Chooser dialo
  • Customize Shape: Lathe3D Editor: opens a modelling tool in which a custom lathed 3D shape may be designed and saved as an OBJ file. There are drop-down menu options on the left for various preset shapes, which may be refined with variant types, scale by X/Y axis to stretch the shape, rotation, view type and tessellation. The shape may be viewed as it is edited in the 3D viewer on the right, in which the shape can be manipulated with the mouse or with buttons to move, rotate, zoom in/out and reset the view of the shape.   
  • Customize Shape: SuperQuadric shape Editor opens a modelling tool in which a custom super-quadric 3d shape may be created and saved as an OBJ file. There are options on the left for various preset shapes, which may be refined with variant types, scale by X/Y axis, rotation, view type and tessellation. The shape may be further altered with the sliders for V and N exponent values, V revolution factor and alpha radius (toroid shape only). The shape may be viewed as it is edited in the 3D viewer on the right, in which the shape can be manipulated with the mouse or with buttons to move, rotate, zoom in/out and reset the view of the shape.   
  • Customize Shape: OBJ Model Loader Shape Editor opens a modelling tool in which a custom OBJ model may be edited. Several pre-set models are provided, which may be edited. An OBJ file, created by 3D modelling software such as Blender or in the Lathe3D and SuperQuadric editor tools described above, may also be loaded. There are options on the left for various preset shapes. A shape from an OBJ file may be loaded by checking Load External OBJ model then clicking the Load button, which opens a file chooser dialogue. The shape may be refined with loader size, scale by X/Y axis to stretch the shape, rotation, view type and tessellation. The shape may be viewed as it is edited in the 3D viewer on the right, in which the shape can be manipulated with the mouse or with buttons to move, rotate, zoom in/out and reset the view of the shape.   
Node Class
  • Node Class: The Containing Class (default New Class) pull down menu enables the user to associate the currently selected node(s) with a Class from the current Class Set. It works in conjunction with the Classes tab, in which the user can define custom Class Sets and Classes.   

Edges Tab

  • Edge Colour button enables the user to select a colour for all graph edges. Selection is done through the Colour Chooser dialog (please refer to Generals tab Options Group 1 for usage details). Note that Colour Edges By should be set to Colour and not to Weight for this option to have any effect.  Options Group 2  
  • Edge Thickness (default value 1.0) drop-down menu gives the user the option to choose a thickness size for all graph edges.  
  • Proportional Edges Size to Weight (default off) checkbox gives the user the option to set size of each edge size as proportional to its weight. Note that this will produce a much slower overall graph rendering speed when used with large graphs.
  • Arrowhead Size (default 5) pull down menu gives the user the option to choose a thickness size for all graph edges arrowheads. Note that arrowheads are only available in 2D mode.  Options Group 4  
  • Colour Edges By (default depending on graph) selection gives the user the option to choose to colour edges either with a pre-set colour (please refer to Option 1 above) or by their associated weight values. N.B. This option only has an effect if weights are available for the current graph.

Classes Tab

Select Current or Create new Class Set & Classes
  • Create Class Set (default empty) textbox/button combination enables the user to create a Class Set with a given name. When a name is inserted into the textbox and the Add Class Set button is clicked, the Class Set name is inserted into to pull down menu of Option 1; it will also be automatically selected as the current one. Duplicate Class Set names are not permitted. Corresponding dialogues will report any successful/erroneous action(s). Note that any comma characters entered in the new Class Set name will be removed. 
  • Create Class (default empty) textbox/button combination gives the user the option to create a Class with a given name, in the current Class Set. The comma character can be used as a delimiter to define multiple Class names to be added in a single action. When a name has been inserted into the textbox and the Add Class button is clicked, the Class name will be inserted into the current Class Set, with an arbitrary colour, and the Class Set Browser will be appropriately updated. Corresponding dialogs will report any erroneous action(s). Note that since comma characters are used for inserting multiple Class names, they cannot be part of a particular Class name.  
  • Select Current Class Set (default Default Classes) drop-down menu enables the user to set the current Class Set. The main graph window will be updated, colouring all the graph nodes with their corresponding Class colours for that Class Set. The Class Set Browser will also be updated, presenting all the available Classes in the current Class Set in  a 3 column table. 
Class Set Browser
  • Class Set Browser table displays all the Classes within the currently selected Class Set. The user can navigate through all of the Classes in the 3 columns table and edit Class colour and name by clicking on the Class colour and the Class name respectively. In particular, clicking on a Class colour presents the Colour Chooser dialogue (please refer to General tabbed options pane window Options Group 1 for details), in which the user can select any colour. Note that all user-defined Class Sets and Classes, along with their respective names and colours, will be saved with all the ‘Save Graph’ options and will be restored when the graph file is re-opened. 

Class Viewer

Class Viewer in Expression Mode

The Class Viewer functions in either Selection Viewer or Class Viewer Mode, depending on the loaded graph. With graphs that do not carry any expression information, Selection Viewer Mode is used; in any other case, the full Class Viewer functionality is used, which incorporates a plot tool for visualizing data associated with the current graph selection.  

The Class Viewer window is a tool for providing detailed information about the current graph selection, as well as data mining on that particular selection. The Class Viewer consists of 3 tabbed panes: General, Analysis and Analysis Detailed.

Selection Viewer Mode

Class Viewer in Selection Mode

General Tab

Option Group 1
  • Render Class Set Plots To Files… button automates multiple Render Plot To File… actions for all the Classes in the current Class Set. A dialogue is shown once to let the user select the folder for the resulting image files as well as the image format (either .png or .jpg). The progress of the process is reported by further dialogues. Note that this option is only available when the full Class Viewer functionality is used, i.e. when the plot component is also displayed within the main Class Viewer dialog window (see Picture 30).  
  • Render Plot To File… button provides functionality to save the current plot component in an image file, for the currently selected Class in the current Class Set. An dialogue is shown once to let the user select the folder in which to save the resulting image files as well as the image format (either .png or .jpg). Note that this option is only available when the full Class Viewer functionality is used, i.e. when the plot component is also displayed within the main Class Viewer dialog window (see Picture 30).  
  • Class Set (default ‘Default Classes’) drop-down menu enables the user to select the current Class Set. The main graph window will be updated with the current Class Set selection, by colouring all the graph nodes with their associated Class colours for that Class Set. The main Class Viewer table will also be updated (please refer to Option 2 below).  
  • Show All Class Sets (default off) checkbox gives the user the option to view all the available Class Sets in Class Viewer. When off, only the current Class Set selected with Option 1 will be presented in the main Class Viewer table (please refer to Option 2 below).  
  • The Hide Unselected Rows button refreshes the current selection in the main Class Viewer table (please refer to Option 2 below). It is mostly useful when the user has deselected/reselected particular nodes in the Selected column of the main Class Viewer table.
  • The Auto Size Columns checkbox causes the table columns to be automatically resized such that they are wide enough to contain the widest item. With this option disabled, the width of the columns is never changed except when the user manually adjusts them.
Option Group 2  

Main Class Viewer Table: The main table of Class Viewer. It consists of multiple rows, each representing a particular node, and data columns with which the user may interact, depending on the particular underlying column’s representation:  

  • Selected column gives the user the option through multiple checkboxes to deselect/reselect particular nodes at will in the current selection. Clicking the Hide Unselected Rows button refreshes the main graph window as well as the main Class Viewer table with the new selection.
  • Name column gives the user the option to view and edit node  names in the current selection.  
  • Connections column gives the user interaction information of how a particular node connects to other nodes.

The rest of the presented columns represent Class Sets and are not editable. The available number of visible columns depends on the underlying loaded Class Set data and whether the Show All Class Sets checkbox is checked.

Option group 3
  • Highlight Is Selection checkbox provides an alternative means of selecting rows. Instead of using the Selected checkbox column, the row selection follows which are highlighted in the table. This enables scrolling through rows using the arrow keys and selecting ranges of rows by clicking and dragging the mouse.
  • Deselect All button unchecks all selected node checkboxes from the main Class Viewer table with one click. When clicked the button changes to Select All, providing the inverse functionality.
Option Group 4
  • Find By Name, Class and Multiple Classes: The Find By Name, Class and Multiple Classes buttons show the Find By Name, Class or Multiple Classes dialogs where the user can interactively search for a given name or class or multiple classes. The resulting node(s) are automatically selected after finishing the name or class search. If no classes are available, the ‘No Class’ selection is the only one available in the class selection drop down menu or table. This Class selection also provides a starting point for the two navigation buttons (please refer to ◄◄ (Previous Class) and ►► (Next Class) options).  
  • ◄◄ (Previous Class) button navigates back through the list of selected Class, to view the Class previous to the current selection, in the Class Viewer. If no previous Class exists, the button is disabled.
  • ►► (Next Class) button navigates forwards through the list of selected Class, to view the Class next to the current selection, in the Class Viewer. If no next Class exists, the button is disabled.
  • When the Search Database button is clicked the Network Import dialog is opened with the keyword field filled with the names of the currently selected nodes. 
Options 5 and 6

Class Viewer specific operations:

  • Choose Columns To Hide button enables the user to control which data columns are displayed in the Class list. The user can hide or unhide columns using the multiple checkboxes in the Columns to Hide dialog. The Deselect All (Option 6) button unchecks all checkboxes. When clicked, the button changes to Select All, providing the inverse functionality. The Hide Window button hides the Columns To Hide dialogue.  
  • Export Table As… button Opens the Export Table As file save dialogue and exports the current view of the main Class Viewer table as a tab-delimited text file.

For some forms of input data a plot tool for visualizing data associated with the current graph selection is displayed.  

  • The Y-axis represents the values of the data (can be of any unit, depending on the loaded expression file).  
  • The X-axis represents the column names used for the data samples (usually mapped to corresponding origin).  
  • Different line colours represent different classes for each of the nodes selected in the main graph view

Expression Data Class Viewer

Class Viewer in Expression Mode

General Tab

Option Group 1

Settings used to customize Expression data representation on the current plot

  • Scaling (default raw) combobox allows rescaling of the input data as follows:
    • Raw - no rescaling
    • Log Scale - convert to logarithmic scale
    • Mean Centred - subtract the mean for the entire row from the value
    • Unit Variance Scaled - as mean centred but divided by the standard deviation
    • Pareto - as mean centred but divided by the square root of the standard deviation  
  • Maximum Samples - the maximum number of samples to display at one time. As this is reduced a scroll bar becomes visible beneath the plot that allows selection of which columns are visible.
  • Grid Lines - (default off) checkbox displays grid lines, making the sample X-axis easier to view.
  • Class Plot - (default Individual Lines) combobox controls the style with which the per-class data is displayed. A variety of line or histogram style plots are available optionally with or without error indication. See below for examples of the different styles of plotting that are available.
  • Selection Plot - (default Individual Lines) combobox serves the same purpose as the class plot option except that it applies to the entire selection rather than per-class.
  • Axes Legend - (default off) checkbox displays a legend of X- and Y-Axis names on the plot.
  • Column Info - a list of column information to display. This includes the sample name and column annotations, if they are available.
Option Group 2

Export Plot Expression Profile As… dialog and saves the current plot’s expression profile to a standard text file (.txt), in a user-selected folder.

If the expression data has column annotations, they can be visualised in the Class Viewer by clicking on the Column Info button and selecting which annotations to display. Each annotation is displayed in a row beneath the plot using colour coded blocks. Each colour corresponds to a particular annotation value. In the example below the annotation Depot is displayed using a range of colours. The blue and pink in the second row correspond to the Source annotation, whilst the red and yellow in the third row correspond to the Sample.Prep annotation. Holding the mouse cursor over the coloured blocks will display a tool tip indicating the annotation value to which it reflects. 

--TODO Picture 

By using the Column Sort option the plot columns can be rearranged such that they are sorted on one of the annotation columns. In this example the data has been sorted on the Source annotation. 

--TODO Picture 

The following screenshots illustrate some of the different ways in which data can be plotted. By clicking and dragging the mouse downwards over a vertical region on the plot, that range will be zoomed. The zoom level is reset by clicking and dragging upwards. Further options may be found by right clicking on the plot and selecting from the context menu. 

Enrichment Tab with results displayed as a table

Enrichment Tab

Graphia Pro provides a suite of tools to check for enrichment of a particular class statistically. Graphia Pro's enrichment analysis uses Fisher's exact test to check the probability of a clusters composition occurring purely by chance. The Enrichment tab contains the configurations options and results of enrichment analyses. It consists of two main panels, a configuration panel on the left and a results panel on the right.

Configuration Panel

The configuration panel displays the number of currently selected nodes at the top, and also displays the total number of unique selected Node classes. If no nodes are selected, enrichment analysis cannot be performed.

Compare Selected Classes - Defines the way in which selected Node classes are analysed. Combined will treat all selected nodes as a large group, while Individually will respect each nodes class and perform analysis on a per-class basis.

Class Set Selector - The class set selector table specifies what Class sets to test for enrichment.

Perform Enrichment Analysis - Performs the enrichment analysis with the specified settings

Results Panel

The results panel contents varies depending on which display mode the results are in. There are three display modes; Table, Heatmap and p-Value charts. By default results are displayed as a table.

Table

The results are displayed as a simple table, with the option to export to a .csv file.

  • Export Table to CSV - Export the currently displayed table results to .csv file
  • Show Only Enriched - Displays only the enriched classes and hides all under-represented or non-enriched values.
  • Display Heatmap - Switches the display mode to Heatmap view.
  • Display P-value Chart - Switches the display mode to p-Value chart view
Heatmap

The results are displayed as a heatmap, this view is useful for visually identifying enriched class sets. The Heatmap displays highly significant results brightly (0 - 0.01), significant results less-so (0.01 - 0.05) and insignificant/unrepresented values dimly. Clicking a cell within the heatmap will navigate to the appropriate table result.

  • Grid lines - Toggle the grid lines on the heatmap image.
  • Save Heatmap - The heatmap will be exported as an image.
  • Display Enrichment Table - Switches the display mode to Table results view.
  • Display P-value Chart - Switches the display mode to p-Value chart view.
p-Value Charts

The results of enriched classes are displayed as Adj. P-value charts. This is useful for comparing multiple enriched results with each other. Clicking a bar will navigate to the appropriate table result.

  • Display Adj. p-Value Charts - Toggles the visibility of the Log axis p-Value charts (Smaller is more significant)
  • Display Scaled Adj. p-Value Charts - Toggles the visibility of the Scaled -Log(p-Value) charts (Larger is more significant)
  • Display Heatmap - Switches the display mode to Heatmap view.
  • Display Enrichment Table - Switches the display mode to Table results view.

Creation of Class Sets and Classes

A Class Set is a means of defining nodes as belonging to different groupings. A Class Set is comprised of one or more Classes to which nodes belong. Once so defined, when a Class Set is selected the nodes belonging to the different Classes will be arbitrarily assigned colours so they can be visibly distinguished/selected in the graph. Examples of Classes in graphs derived from biological relationships might be Gene Ontology terms, statistical hits, genes of interest, species of origin, protein type etc.  Each node may belong to only one Class within a Class Set.  A file may have any number of associated Class Sets, each of which can contain any number of Classes. It is not required that all nodes are assigned as belonging to a Class in any given Class Set, with nodes not assigned belonging to the class ‘No Class’.

Class sets and classes may be created in a number of ways:       

Assignment of Class Sets within Graphia Pro

Nodes may be assigned to classes within the application.   

  • To create a new Class Set:   
    • In Graph Properties, open the Classes Tab.   
    • Enter the name of the new Class Set in the text field labelled Create Class Set.     
    • Click the Add Class Set button; the new Class Set is automatically selected as the current one.   
  • To create a new Class in the current Class Set: o Enter the name of the new Class in the Create Class text field.    
    • Alternatively, a comma character can be used as a delimiter to define multiple Class names to be added in one action.    
    • Click the Add Class button; the Class names are inserted into the current Class Set, each with an arbitrary chosen colour; the new Classes are listed in the Class Set Browser.  
  • To place nodes in any of the newly created Class Sets: o Select nodes of interest from the graph.
    • In Graph Properties, open the Nodes Tab.   o At the bottom of this dialog is a drop-down menu which contains a list of all the Classes that have just been created.  Choose the one into which you wish to place the selected nodes and click Apply. Those nodes are now assigned to the selected Class.  
  • Assigning Nodes to Cluster Class Sets.  One of the great features of Graphia Pro is the ability to cluster graphs based on their topology and, where available, edge weights, using the MCL clustering algorithm:
    • In Graph Properties, open the MCL tab.
    • Enter values for Inflation, Pre-Inflation, Scheme and Smallest Cluster Allowed.
      • Click Apply.
      • Click Cluster Graph Using MCL.
    • Following clustering, nodes are assigned to clusters. A new Class Set is created, with a Class for each cluster. The Class Set appears in the Select Current Class Set drop down with the naming convention MCL_inflation_scheme where inflation is the inflation value and scheme is the scheme value, for example MCL_4.4_5 where inflation is 4.4 and scheme is 5.
    • If the graph is saved the cluster Class Sets will be preserved in the layout file.

Perhaps the simplest means of defining Class Sets associated with data is to import assignments directly in the graph import file. Built into the "correlation" format is the ability to assign nodes to Class Sets by including columns between the node identifier column and the data columns which are used to generate the correlation matrix used for graph definition (see above).

To select one of the imported Class Sets for display:  

  • Open the Classes tab in Graph Properties.  
  • Select the required Class Set from the Select Current Class Set drop-down.  
  • Click Apply. 

Class Set Definition within .layout and .txt Files

Creating classes in the pairwise file formats is straightforward. Below the definition of edges in the file, named nodes can be assigned to a specific Classes within Class Sets as follows:

. NodeID Class Class Set
//NODECLASS NodeA “Transcription factor” “Protein function”
//NODECLASS NodeA “Human” “Species”
//NODECLASS NodeB “Kinase” “Protein function”
//NODECLASS NodeB “Mouse” “Species”

The example above will create two new Class Sets (Protein function and Species). NodeA will be assigned an annotation of Transcription factor in the protein function Class Set and to Human in the Species Class Set. NodeB will be assigned an annotation of Kinase in the protein function Class Set and to Mouse in the Species Class Set. The above annotation lines should be appended at the bottom of the input file, following the edge descriptions. If definitions do not contain spaces, they can be tab-delimited. However if definitions contain spaces, annotations should be enclosed with double quotes (as shown).

New classes within a Class Set are automatically assigned a random colour. Classes may also be assigned colours in the input file. To assign a colour to a Class, add a line containing the desired colour at the end of an input file as follows:    

Class Name Class Set Name Colour
//NODECLASSCOLOR “Human” "Species" "#FF0000"

Node Properties

A number of node properties can also be directly encoded into the input file. Such properties include: Size, Colour and Position of nodes. The following examples illustrate how to change various properties for a node called ‘NodeA':

Node Position

Class Name Node Position in X, Y, Z coordinates
//NODECOORD NodeA 100.0 500.0 400.0

Sometimes it is desirable for a the position of a node to be fixed during the layout process. It is also possible to import coordinates for the layout of nodes, generated by other packages. To fix the position of a node add X,Y and Z coordinates as shown above. In this case NodeA is assigned to a position of (100.0, 500.0, 400.0) in X, Y, Z space. The Graphia Pro layout space is (1000.0, 1000.0, 1000.0). If one desires a 2D layout, setting the Z coordinate to 500.0 will keep the node on the central Z plane.  

Node Size

Node Name Node Size in Units
//NODESIZE NodeA 16

This sets the size of NodeA to 16 units. Node sizes are rendered according to how many nodes are present in a graph, so some experimentation may be required to determine an appropriate size.  

Node Shape

Node Name 2D Node Shape 3D Node Shape
//NODESHAPE NodeA 16 0

This example sets the shape of NodeA to a circle in 2D and a sphere in 3D. See the table below for a list of codes and shapes. Shapes may also be adjusted in the Nodes tab of Graph Properties.  

Code 2D Shape 3D Shape
0 Circle Sphere
1 Rectangle Point
2 Round Rectangle Cube
3 Triangle Tetrahedron
4 Diamond Octahedron
5 Parallelogram Dodecahedron
6 Hexagon Icosahedron
7 Octagon Cone Left
8 Trapezoid1 Cone Right
9 Trapezoid2 Trapezoid Up
10 Rectangle Vertical Trapezoid Down
11 Rectangle Horizontal Cylinder
12 Torus
13 Rectangle Vertical
14 Rectangle Horizontal
15 Round Cube Large
16 Round Cube Thin
17 Gene Model
18 Pineapple Slice Toroid
19 Pineapple Slice Ellipsoid
20 Double Pyramid Thin
21 Double Pyramid Large
22 Torus 8 Petals
23 Saucer 4 Petals
24 Lathe3D
25 SuperQuadric
26 OBJ Model Loader

Node Alpha

Node Name Node Alpha transparency (0.0-1.0 range)
//NODEALPHA NodeA 0.5

This sets the alpha transparency value of NodeA to 0.5 (half transparent). The alpha transparency value is a decimal number in the range of 0.0-1.0. A lower value makes the node more transparent. The value is only used when the Transparency option is turned on in the Nodes tab.            

Pathway Commons Client

A client to query and download pathways from the Pathway Commons pathway resource is available to Graphia Pro.  Pathway Commons is a publically available resource that aggregates pathway and interaction data from a range of databases into linked data. Pathways are downloaded and visualised as BioPAX level 3 OWL files (see Data Input Formats).

To open the client, go to File > Import > Search Pathway Commons... 

Search

  • Keywords: Keywords are entered into the Keyword field.  To restrict the search to the BioPAX pathway name only (as opposed to all text associated with pathway), leave the Name checkbox ticked.  To perform a full text search, uncheck the Name checkbox; search terms may be separated with Boolean operators AND/OR. A specific search field may be combined with a search term separated by a colon; these are: comment, ecnumber, keyword, name, pathway, term, xrefdb, xrefid, dataSource and organism. Wildcards may be searched using an asterisk. For example, the search string:
name:kinase AND pathway:signal*

searches for signalling pathways that include “kinase” in their names.

  • Organism: NCBI ID number or species name may be entered in the text field.  For convenience, popular species may be searched for using the provided checkboxes.
  •   Data Source: The databases from which Pathway Commons aggregates information are listed as checkboxes that may be used to restrict the search.
  • Type: Dropdown list defines which BioPAX type to search for: Pathway, Interaction, Physical Entity, Entity Reference.  There is an additional option, Top Pathways, which is a special case; this is defined as “pathways that are neither 'controlled' nor 'pathwayComponent' of another process”.

Click the Search button to perform the search. The Stop button may be used to terminate a search process before it has completed if it is taking too long to complete. Search results are displayed in the table. Results are returned in pages of 500 search hits; the sequence of pages may be navigated using the Next/Previous buttons.

Click on a row in the results table to display detailed information about that network in the pane on the right hand side.  Information includes the species name retrieved from the NCBI taxonomy service and a count of the number of Interactions in the network, derived from a traverse query, to give an indication of the size of the network.   

Click the Open button to download and display the network for the search hit you have highlighted in the results table. In the special case of Interaction, the nearest neighbourhood of the interaction is opened with limit 1.  

If you wish to use the search hit to perform an advanced graph query, double click the row in the results table and the search hit will be added to the Advanced tab.   

Advanced

The Advanced tab of the Import Network dialogue enables you to perform advanced graph queries on search hits retained from search results. Options are:

  • BioPAX Query Type:
    •    Get – retrieve multiple search hits as a single network graph
    •    Nearest Neighborhood - search neighborhood of a given source set of nodes with length limit 1
    •    Common Stream - search common downstream or common upstream of a specified set of entities based on the given directions within the boundaries of length limit 1
    •    Paths Between - find the paths between specific source set of states or entities within the boundaries of length limit 1
    •    Paths From To - find the paths from a specific source set of states or entities (highlighted rows) to a specific target set of states or entities (non-highlighted rows) within the boundaries of length limit 1. Highlight rows with Control-click (Windows) or Command-click (Mac).
  •   Direction – defines the graph search direction
    •   Downstream
    •    Upstream
    •    Both - searches upstream and downstream