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gographviz [2010/06/02 21:28]
sgoetz
gographviz [2010/06/02 21:29] (current)
sgoetz
Line 22: Line 22:
 {{ :​example_data:​gographviz:​graph2.jpg?​750 |Graph colored by a user defined score}}\\ ​ {{ :​example_data:​gographviz:​graph2.jpg?​750 |Graph colored by a user defined score}}\\ ​
  
-====== Examples ====== 
  
 +==== Input Parameters ====
  
 +  * **Association File**: A tabulator separated file indicating first the Annotation Unit (a sequence, a cluster, a gene set, etc.) and than the GO-term(s). As a third column a score value  (0-1) can be set optional and is used for coloring issues when graph-coloring mode "input score" is selected.
 +
 +**File format example**
 +<​file> ​  ​Seq1 GO:​0000001 0.1
 +   ​Seq2 GO:​0000011 0.8
 +   ​Seq3 GO:​0000015 0.6
 +   ​Seq4 GO:​0000015 0.12
 +   ​Seq5 GO:​0000027 0.45
 +   ...
 +   ​...</​file>​
 +
 +
 +  * **GO Category**: The GO category you wish to visualize.
 +  * **ID Node Filter:** Filter out GO-terms with less then the given number of annotation units assigned.
 +  * **Mode of Graph-Coloring:​** Select which graph feature to visualize.
 +    * **ID-count:​** Colorize by the number of IDs united at a term.
 +    * **Annot-score:​** Colorize by the Annot-Score of a term. 
 +    * **Input-score:​** Colorize by the score defined in the input file.
 +  ​
 +  * **Annot-Score parameter:​** This parameter adjusts the alpha of the Annot-Score formula (GO Annot-Score = sum( number_of_ids x exp( alpha, distance to origin)))
 +  * **Annot-Score Node Filter:** Thin out graphs by the Annot-Score. ​
 +  * **Color:** Main graph color (at the moment disabled)
 +
 +==== Output ====
 +
 +Several images (jpg, svg, png) of the generated graph are given as Output. The graphs can also be downloaded in form of a textual representation. Further, a link (.jnlp) starts automatically the interactive graph visualization tool in form of a Java Web Start application.
 +
 +
 +====== Examples ======
 ===== Example 1 ===== ===== Example 1 =====
  
Line 52: Line 81:
 {{:​example_data:​gographviz:​gographviz_goscores.txt|An association file example which simply visualizes a list of gene ontology terms with an associated intensity value}} {{:​example_data:​gographviz:​gographviz_goscores.txt|An association file example which simply visualizes a list of gene ontology terms with an associated intensity value}}
  
-==== Input Parameters ==== 
  
-  * **Association File**: A tabulator separated file indicating first the Annotation Unit (a sequence, a cluster, a gene set, etc.) and than the GO-term(s). As a third column a score value  (0-1) can be set optional and is used for coloring issues when graph-coloring mode "input score" is selected. 
- 
-**File format example** 
-<​file> ​  ​Seq1 GO:​0000001 0.1 
-   ​Seq2 GO:​0000011 0.8 
-   ​Seq3 GO:​0000015 0.6 
-   ​Seq4 GO:​0000015 0.12 
-   ​Seq5 GO:​0000027 0.45 
-   ... 
-   ​...</​file>​ 
- 
- 
-  * **GO Category**: The GO category you wish to visualize. 
-  * **ID Node Filter:** Filter out GO-terms with less then the given number of annotation units assigned. 
-  * **Mode of Graph-Coloring:​** Select which graph feature to visualize. 
-    * **ID-count:​** Colorize by the number of IDs united at a term. 
-    * **Annot-score:​** Colorize by the Annot-Score of a term.  
-    * **Input-score:​** Colorize by the score defined in the input file. 
-  ​ 
-  * **Annot-Score parameter:​** This parameter adjusts the alpha of the Annot-Score formula (GO Annot-Score = sum( number_of_ids x exp( alpha, distance to origin))) 
-  * **Annot-Score Node Filter:** Thin out graphs by the Annot-Score. ​ 
-  * **Color:** Main graph color (at the moment disabled) 
- 
-==== Output ==== 
- 
-Several images (jpg, svg, png) of the generated graph are given as Output. The graphs can also be downloaded in form of a textual representation. Further, a link (.jnlp) starts automatically the interactive graph visualization tool in form of a Java Web Start application. 
gographviz.txt ยท Last modified: 2010/06/02 21:29 by sgoetz
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