Difference between revisions of "Guide/Matrix"
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− | + | Mx matrices are best viewed using Firefox. Get Firefox [http://www.mozilla.com/en-US/firefox/upgrade.html here]. | |
+ | |||
+ | == Introduction == | ||
+ | [[http://hymenoptera.tamu.edu/wiki/index.php/App/mx#show Matrices]] in mx display the intersection of a series of characters and OTUs set to public by the matrix owner. | ||
+ | == Overview of functionality == | ||
+ | Shows the matirx, one click view for matrix cells, nexus and tnt file export, link to views for tags, characters and OTUs. | ||
+ | == Definitions == | ||
+ | * '''OTUs''' (Operational Taxonomic Units) are the taxa being compared. | ||
+ | |||
+ | == Navigating the page == | ||
+ | [[Image:Matrix.jpg]] | ||
+ | |||
+ | 1. Number of OTUs and Characters in the matrix. | ||
+ | |||
+ | 2. Click on a matrix cell and the OTU, Character and State information will display above the matrix. | ||
+ | |||
+ | 3. Links to other display pages including: | ||
+ | * '''characters''' - a list of characters in the key which link to detailed descriptions of character/character states. Includes images and figures. | ||
+ | * '''grid tags''' - Mx [[http://hymenoptera.tamu.edu/wiki/index.php/App/tag#index tags]] are combination of a user defined keyword and an "object" (anything with a primary_id, such as an OTU, character, character state, coding, image, collecting event, specimen etc.) in mx. Within a tag an optional linkage to a reference and a custom notes/value field are also available. Tags are great way to group objects within mx, or communicate notes etc. | ||
+ | * '''trees''' - Link to [[http://hymenoptera.tamu.edu/wiki/index.php/App/tree#index trees]] associated with this public matrix. Mx can store phylogenetic trees. Both Newick formatted strings (a simple text field) and a fully parsed set of nodes are stored in the database. While there is currently minimal functionality for using the parent/child data the system provides a good starting point for those wishing to develop query based methods on trees. | ||
+ | |||
+ | 4. Matrices are exported in nexus and tnt formats. | ||
+ | * '''save as file''' - downloads directly to your computer. The other print to the screen. Cut and paste the text and save as a file. | ||
+ | |||
+ | 5. Change the size of a matrix display to accommodate any size screen. This functionality is particularly important with larger matrices. | ||
+ | |||
+ | 6. Links to the home page and help topics for a page. | ||
+ | |||
+ | 7. Click on an OTU in a matrix takes you to a OTU show page. | ||
+ | |||
+ | 8. Click on a character takes you to a character show page. |
Latest revision as of 14:59, 31 August 2009
Mx matrices are best viewed using Firefox. Get Firefox here.
[edit] Introduction
[Matrices] in mx display the intersection of a series of characters and OTUs set to public by the matrix owner.
[edit] Overview of functionality
Shows the matirx, one click view for matrix cells, nexus and tnt file export, link to views for tags, characters and OTUs.
[edit] Definitions
- OTUs (Operational Taxonomic Units) are the taxa being compared.
[edit]
1. Number of OTUs and Characters in the matrix.
2. Click on a matrix cell and the OTU, Character and State information will display above the matrix.
3. Links to other display pages including:
- characters - a list of characters in the key which link to detailed descriptions of character/character states. Includes images and figures.
- grid tags - Mx [tags] are combination of a user defined keyword and an "object" (anything with a primary_id, such as an OTU, character, character state, coding, image, collecting event, specimen etc.) in mx. Within a tag an optional linkage to a reference and a custom notes/value field are also available. Tags are great way to group objects within mx, or communicate notes etc.
- trees - Link to [trees] associated with this public matrix. Mx can store phylogenetic trees. Both Newick formatted strings (a simple text field) and a fully parsed set of nodes are stored in the database. While there is currently minimal functionality for using the parent/child data the system provides a good starting point for those wishing to develop query based methods on trees.
4. Matrices are exported in nexus and tnt formats.
- save as file - downloads directly to your computer. The other print to the screen. Cut and paste the text and save as a file.
5. Change the size of a matrix display to accommodate any size screen. This functionality is particularly important with larger matrices.
6. Links to the home page and help topics for a page.
7. Click on an OTU in a matrix takes you to a OTU show page.
8. Click on a character takes you to a character show page.