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From PathVisio Wiki
Overview
PathVisio is a tool for displaying and editing biological pathways. In a sense PathVisio lets you draw pathways as though you are drawing them in powerpoint. But the difference is that PathVisio can understand the biological context of a pathway, because you can link biological components (genes or proteins) in your pathways to biological data using database identifiers. This will let you map experimental data (e.g. microarray data) and visualize it on top of the pathway drawing (Note: mapping experimental data is not yet a feature of PathVisio 1.0, but you can do this in combination with GenMAPP).
Here is a screenshot of the program in action:
Editing pathways
How do I ... Create a new pathway?
- Create a new pathway by pressing Ctrl+N or going to File > New Pathway.
- A blank drawing area will open where you can start adding and editing new elements. Specific editing features are described below.
Edit mode
PathVisio distinguishes between simple viewing and editing pathways through the use of the edit mode. To begin editing a pathway, first make sure you are in edit mode. You can turn on and off edit mode in the Edit menu.
Placing new objects
Add new objects by selecting one of the object icons in the toolbar, then drag and drop the object in the desired location in the drawing area. Note that the object icons are only available in edit mode. If you're unsure what a certain icon does, you can hover over it with the mouse cursor to get a description.
Selecting objects
Single or multiple objects can be selected in two ways:
- Click-and-drag anywhere in the drawing area and drag to select any number of objects using a rectangular selection tool.
- Click on any object to select it. Holding down the Ctrl key and click on additional items to add these to the selection.
Moving objects
You can move objects in two ways:
- Click and drag: Select one or more objects and then click and drag the selection to the desired location.
- Arrow keys: Select one or more objects and click any of the keyboard arrow keys to move the selected objects. Holding down the shift key while pressing the arrow keys will move the objects with a larger increment.
Changing the size of objects
You can change the size of objects in two ways:
- Click on an object and drag the handles to resize or move objects.
- Open the properties tab in the panel on the right side of the window. Change the size of the object by entering information for Width and Height.
Pathvisio in edit mode:
Grouping objects
PathVisio supports the notion of groups, to facilitate editing and for describing biological entities. Any selection of objects can be grouped in PathVisio:
- Select the group of objects to be grouped.
- Click Ctrl+G to group the objects. The objects can now be moved as a group and the group can also be linked to other objects. Clicking Ctrl+G again ungroups the group.
Groups can be nested so that a larger group can contain other groups. Ungrouping works on the top-level grouping only, so to completely ungroup several nested groups ungroup has to be performed for each group
Aligning, scaling and stacking objects
To facilitate editing, objects can be aligned, scaled and stacked using a set of buttons in the toolbar.
- Align vertically: Center of objects are aligned vertically based on the location of the top selected object
- Align horizontally: Center of objects are aligned horizontally based on the location of the top selected object
- Set common width: Widths of selected objects are set to the width of the widest selected object
- Set common height: Heights of selected objects are set to the height of the tallest selected object
- Stack vertically: Objects are are arranged into a vertical stack based on the top selected object
- Stack horizontally: Objects are are arranged into a horizontal stack based on the top selected object
Zoom
Pathways can be zoomed using the zoom drop-down in the toolbar or by going to View > Zoom. The Zoom to fit option sizes the pathway to fit in the current drawing area.
Copy and paste
Copy and paste works for objects within a given pathway as well as between pathways open in different windows of PathVisio. Copy and Paste can be accessed in the Edit menu as well as with shortcut keys, Ctrl+C copies selected objects and Ctrl+V pastes copied objects.
Linking two biological entities together
You can link any line endpoint to a shape, gene product or brace in the following way:
- Click on the line and select the end point handle
- While holding down the Alt key, drag the end point to the object you want to the object you want to link it to. When a green outline appears around the object, release the handle.
The end point of the line is now tied to the object. If you move the object, the endpoint of the line follows. However, you can still move the line independently of the shape.
Adding references to database identifiers
When creating a pathway, it is useful to link the genes to public database identifiers. To do this, you must first select one the synonym databases distributed by PathVisio:
- Download and install the synonym database you want to use (How?).
- Go to Data > Select Gene Database and choose the database file you want to use. The status bar at the bottom of the PathVisio window will show which gene database is currently used.
- Select the gene product for which you want to enter an identifier.
- In the property panel on the right side of the PathVisio main window, enter the database identifier in the "Name" property, and select the database the identifier belongs to from the System Code property.
Editing object properties
In the property panel on the right side of the PathVisio window you have precise control over all the properties of the object you have currently selected. For example, you can position objects by entering exact coordinates, change their color or size. You can also change the font and style of labels, or add notes to any object. For a lot of properties, editing them in the property panel is the only way to change them. Not all object types have the same set properties, for example, only Gene products have the "Gene ID" property.
To edit a certain property, double-click on the entry in the table of properties to make the field editable, then enter the desired value.
It is possible to select multiple objects at once, and edit one property for all of them.
Changing the size of the drawing area
You can access the pathway properties by clicking on the pathway info object. The pathway info object appears in the top left of a new pathway. Click on it to select it and change the values for the boardwidth and boardheight properties in the property tab.
Importing and exporting to / from GenMAPP
You can import/export your pathway from and to the GenMAPP format (.mapp).
- To import a GenMAPP pathway, go to File > Import and select the GenMAPP file you want to import. The pathway will now be loaded in PathVisio where you can edit it and save it to the GPML format, or export it back to a GenMAPP file.
- To export your PathVisio pathway to a pathway file that can be read by GenMAPP, go to File > Export. Specify the GenMAPP file you want to save the pathway to.
Browsing Pathways
Searching pathways for genes
PathVisio allows you to search for pathways that contain a given gene product. You can search pathways in two ways:
- Gene symbol (gene name)
- Gene identifier (as defined in the synonym database)
Search by gene symbol
This method searches for all pathways containing one or more gene products for which the gene symbol contains the specified search text. To find only gene products where the symbol exactly matches the search text, add "\b" before and after the text (e.g. "\bTP53\b" to search for exact matches of "TP53"). To start the search, go to the Pathway search tab in the side panel:
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You can choose to search by gene symbol or gene id using the drop-down list (red arrow). This screen shot shows how to search by gene symbol:
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Search by gene identifier
This method searches for all pathways containing one or more gene products that correspond to the given identifier. Gene products that are linked via cross references in the synonym database are also included. To start the search, go to the Search tab in the side panel:
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You can choose to search by gene identifier using the drop-down list (red arrow). This screen shot shows how to search by gene identifier:
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Browsing search results
The search results will be displayed in the side panel. For example, results of a gene symbol search for "TNF" in all human pathways will look like this:
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The results table (yellow box) shows the pathway that have one or more gene-products with a symbol that contains "TNF". If you double-click on a pathway in the table, PathVisio will open this pathway and highlight the gene products that were found (here the gene products are highlighted with a green box). You can disable this highlighting by unchecking highlight found genes (red arrow). |
Retrieving Databases and Pathways
Downloading and Installing pathways
In the download section on the Main Page you can find a link to zip files containing available pathways converted from GenMAPP. After you download one or more of these zip files, unpack them to the PathVisio\pathways folder in your user directory (e.g C:\Documents and Settings\Username\Pathvisio\pathways on windows XP). This is the default folder where Pathvisio looks for pathway files.
Downloading and Installing synonym databases
Gene Databases provide PathVisio with cross references between gene identifiers in pathways and other database identifiers. Databases are downloaded and installed locally for use with PathVisio. In step 3 in the download section you can find a link to these databases. Download and unzip databases to the Pathvisio\gene databases directory in your user directory on your computer. Be warned: gene databases can take up a lot of disc space. For the human gene database you need at least 400 Mb of free disk space.
Available synonym databases
Our synonym databases contain the latest information from Ensembl. A synonym database for any species that is in Ensembl can be generated. You can get the available synonym databases from the download page. If you would like to have a PathVisio synonym database for another species that is present in Ensembl, please contact us.
Supported database systems
Each supported public database supported in PathVisio synonym databases has a specific system code that is used to identify which system a particular identifier belongs to in PathVisio. The following list displays the proper system codes for PathVisio:
| D | SGD (S. cerevisiae) |
| Em | EMBL |
| En | Ensembl |
| H | HUGO |
| I | InterPro |
| L | Entrez Gene |
| M | MGI (M. musculus) |
| Om | OMIM |
| Pd | PDB |
| Pf | Pfam |
| Q | RefSeq |
| R | RGD (R. norvegicus) |
| S | Uniprot/TrEMBL |
| T | Gene Ontology |
| U | UniGene |
| X | Affymetrix Probe Set ID |
| O | Other, for use with a custom database |
Other Features
Setting Preferences
Several preferences can be set in PathVisio to customize the appearance and usage of the program. The Preferences menu can be accessed from the View menu. Options in the Preferences menu are:
Display
- The initial size of the right side panel when PathVisio is first opened can be set. The default value for this is 30.
- Gene product rectangles (data nodes) can be displayed with rounded or squared edges. The default is squred edge display.
- Movement of lines on the drawing board can be either be free or lines can be set to "snap-to-angles" to facilitate drawing. The default is free movement. The degree of angles for "snap-to-angle" is user-defined as well, the default is 15.
- Support for MIMs (Molecular Interaction Maps) can be loaded automatically when PathVisio starts. MIMs support is not loaded by default.
- Advanced object attributes, such as references, can be displayed. Advanced attributes are hidden by default.
- Coloring preferences for managing the coloring of highlighted and selected objects, as well as options for coloring related to displaying data. NOTE: Displaying data on pathways is not currently a feature of PathVisio 1.0.
- Default color for "no criteria met"
- Default color for "gene not found"
- Default color for "no data found"
- Outline color for selected objects
- Outline color for highlighted objects
Directories
Preferences for file locations determine in which directories PathVisio will look for files by default. The following file locations can be set:
- gpml pathways
- Gene databases
- Expression Datasets (NOTE: PathVisio 1.0 does not currently support displaying data on pathways)
Files
The location of where the PathVisio log file will be stored can be set as a preference.
Database
The type of database connector for gene databases and expression datasets can be stored as a preference. NOTE: PathVisio 1.0 does not currently support the display of data on pathways.
Keyboard shortcuts
Ctrl + N: Create a new pathway
Ctrl + O: Open a pathway
Ctrl + S: Save pathway
Ctrl + C: Copy
Ctrl + V: Paste
Ctrl + left mouse click: Add or remove object from selection
Ctrl + A: Select all gene products on the pathway
Ctrl + G: Create a group of selected objects
Ctrl + Z: Undo
