GeWorkbench-web/Cellular Networks KnowledgeBase tmp - Revision history

Smith: /* Display */

2016-09-22T20:38:18Z

‎Display

2016-09-22T20:36:37Z

‎Display

2016-09-22T20:26:39Z

‎Display

2016-09-22T20:23:34Z

‎Controls

2016-09-22T20:12:06Z

‎Export

2016-09-22T20:09:52Z

‎Export

2016-09-22T19:58:51Z

‎Layout managers

2016-09-22T19:57:39Z

‎Layout managers

2016-09-22T19:52:47Z

‎Layout managers

2016-09-22T19:52:27Z

‎Layout managers

← Older revision		Revision as of 20:38, 22 September 2016
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−	* '''t-test''' - project the results of a t-test onto the displayed network. You will be prompted to choose an existing t-test result node from the Worksapce. Nodes showing overexpression are colored red, and underexpressed nodes are colored blue.	+	* '''t-test''' - project the results of a t-test onto the displayed network. You will be prompted to choose an existing t-test result node from the Worksapce. Nodes showing overexpression are colored red, and underexpressed nodes are colored blue. The shade of red or blue becomes darker with increasing over- or under-expression.

	* '''reset''' - remove the t-test display.		* '''reset''' - remove the t-test display.

← Older revision		Revision as of 20:36, 22 September 2016
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−	* '''t-test''' - project the results of a t-test onto the displayed network. You will be prompted to choose an existing t-test result node from the Worksapce.	+	* '''t-test''' - project the results of a t-test onto the displayed network. You will be prompted to choose an existing t-test result node from the Worksapce. Nodes showing overexpression are colored red, and underexpressed nodes are colored blue.

	* '''reset''' - remove the t-test display.		* '''reset''' - remove the t-test display.

← Older revision		Revision as of 20:26, 22 September 2016
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	===Display===		===Display===

−	[[Image:CNKB_Cytoscape_0.7_t-test.png\|thumb]]	+	[[Image:CNKB_Cytoscape_0.7_t-test.png\|thumb\|none]]

@@ Line 176: / Line 176: @@
 ===Display===
 * '''t-test''' - project the results of a t-test onto the displayed network.  You will be prompted to choose an existing t-test result node.
 * '''reset''' - remove the t-test display.

@@ Line 172: / Line 172: @@
 ===Export===
 The network will be exported to a file as an adjacency matrix using gene symbols.
-* '''Save as ADJ''' - save the network in the geworkbench adjacency matrix format.
+* '''Save as ADJ''' - save the network in the geworkbench [[File_Formats#Adjacency_matrix_(ADJ)_format|adjacency matrix]] format.
-* '''Save as SIF''' - save the network in the Cytoscape SIF format.
+* '''Save as SIF''' - save the network in the [[File_Formats#SIF_format|Cytoscape SIF]] format.
 ===Display===

@@ Line 133: / Line 133: @@
 ===Export===
 * '''Export table to Excel''' - The full tabular data is exported to an Excel format (.xls) file in the same format as it is displayed.
-* '''Export interactions to SIF''' - Export interactions, with their interaction types, to a Cytoscape SIF format file.
+* '''Export interactions to SIF''' - Export interactions, with their interaction types, to a [[File_Formats#SIF_format|Cytoscape SIF]] format file.
-* '''Export interactions to ADJ''' - Export interactions, with their values (e.g. probability), to a geWorkbench adjacency matrix file.
+* '''Export interactions to ADJ''' - Export interactions, with their values (e.g. probability), to a geWorkbench [[File_Formats#Adjacency_matrix_(ADJ)_format|adjacency matrix]] file.
 =Cytoscape Display of Network=

@@ Line 147: / Line 147: @@
 ===Layout managers===
 Several different layout managers are available with which to draw the network.  Often the most useful is "cose".
 [[Image:CNKB_Cytoscape_0.9_concentric.png|thumb|left|concentric]]

@@ Line 151: / Line 151: @@
 [[Image:CNKB_Cytoscape_0.9_grid.png|thumb|none|grid]]
 [[Image:CNKB_Cytoscape_0.9_circle.png|thumb|left|circle]]
 [[Image:CNKB_Cytoscape_0.9_cose.png|thumb|none|cose]]
 [[Image:CNKB_Cytoscape_0.9_breadthfirst.png|thumb|none|breadthfirst]]