Cytoscape Network Viewer - Revision history

Smith: /* Layout of the Cytoscape component */

2014-04-17T21:48:53Z

‎Layout of the Cytoscape component

Smith at 20:11, 22 January 2014

2014-01-22T20:11:19Z

Smith: /* Cytoscape VizMapper tab - set shapes and color */

2013-09-25T17:24:45Z

‎Cytoscape VizMapper tab - set shapes and color

Smith: /* Edges colored by interaction type */

2013-09-25T17:22:17Z

‎Edges colored by interaction type

Smith: /* Edges colored by interaction type */

2013-09-25T17:21:33Z

‎Edges colored by interaction type

Ut2102: /* Create subnetwork */

2013-07-16T19:02:37Z

‎Create subnetwork

Ut2102: /* Create subnetwork */

2013-07-16T19:02:19Z

‎Create subnetwork

Ut2102: /* Cytoscape VizMapper tab - set shapes and color */

2013-07-16T19:01:44Z

‎Cytoscape VizMapper tab - set shapes and color

Ut2102: /* Apply Visual Style */

2013-07-16T19:01:22Z

‎Apply Visual Style

Ut2102: /* Changes in Cytoscape 2.8 */

2013-07-16T19:00:28Z

‎Changes in Cytoscape 2.8

@@ Line 47: / Line 47: @@
 # At lower left is a navigation tool which shows the entire network and the location and size (purple rectangle) of the current viewing pane.  The purple viewing pane can be moved about the network as desired. This is done by left-clicking with the mouse in the purple rectangle and moving it.
 # At lower right, nodes or edges that have been selected in the network display will appear in the Data Panel.
 ==Changes in Cytoscape 2.8==

@@ Line 3: / Line 3: @@
 ==Overview==
-Cytoscape  (www.cytoscape.org) is a sophisticated network and pathway visualization tool that has been incorporated into geWorkbench as a component.  Within geWorkbench, Cytoscape is used to depict putative interaction networks, for example as created from running ARACNe or a Cellular Network Knowledge Base query.  Both of these tools return "adjacency matrices", that is, interaction networks, to the Project Folders component.
+Cytoscape  (www.cytoscape.org) is a sophisticated network and pathway visualization tool that has been incorporated into geWorkbench as a component.  Within geWorkbench, Cytoscape is used to depict putative interaction networks, for example as created from running ARACNe or a Cellular Network Knowledge Base query.  Both of these tools return "adjacency matrices", that is, interaction networks, to the [[Workspace|Workspace]].
 Cytoscape has been integrated into geWorkbench in such a way that it can communicate in both directions with the Markers component.
@@ Line 33: / Line 33: @@
 ==Gene Level Summarization of Networks==
-If the network to be viewed is represented by e.g. Affymetrix probesets, and if an appropriate annotation file has been loaded, then geWorkbench will summarize the network at the gene level before displaying it using Cytoscape.  A gene may be represented by more than one probeset. All edges connected to probesets representing one gene are assigned to a single gene node.  This may cause the number of nodes and edges displayed in Cytoscape to be less than those in the original probeset-level network.  You can see the number of nodes and edges in the original network by hovering the mouse cursor over the network data node in the Project Folders component.
+If the network to be viewed is represented by e.g. Affymetrix probesets, and if an appropriate annotation file has been loaded, then geWorkbench will summarize the network at the gene level before displaying it using Cytoscape.  A gene may be represented by more than one probeset. All edges connected to probesets representing one gene are assigned to a single gene node.  This may cause the number of nodes and edges displayed in Cytoscape to be less than those in the original probeset-level network.  You can see the number of nodes and edges in the original network by hovering the mouse cursor over the network data node in the [[Workspace|Workspace]].
 ==Layout of the Cytoscape component==
@@ Line 295: / Line 295: @@
 ===Destroy Network===
-Completely remove the network from Cytoscape.  Note that this does not remove the network adjacency matrix from the geWorkbench Project Folders component.  The network can be recreated in Cytoscape by clicking on the appropriate adjacency matrix in the Project Folders component.
+Completely remove the network from Cytoscape.  Note that this does not remove the network adjacency matrix from the geWorkbench [[Workspace|Workspace]].  The network can be recreated in Cytoscape by clicking on the appropriate adjacency matrix in the [[Workspace|Workspace]].
 ===Apply Visual Style===
@@ Line 369: / Line 369: @@
 ===Show t-test results===
 ====Description====
-When a t-test has been run in geWorkbench, its results are placed in a child data node under the parent dataset in the Project Folders component.  The results (in terms of a p-value calculated from the t-statistic for each marker) can be viewed as a "heat map" using the Color Mosaic component, or as a Volcano plot.
+When a t-test has been run in geWorkbench, its results are placed in a child data node under the parent dataset in the [[Workspace|Workspace]].  The results (in terms of a p-value calculated from the t-statistic for each marker) can be viewed as a "heat map" using the Color Mosaic component, or as a Volcano plot.
 geWorkbench can also overlay t-test results onto a network displayed in Cytoscape.  Genes which have a significant (above threshold) result in the t-test and which are present as nodes in the network can be colored according to the sign and magnitude of the marker t-statistic. Positive t-statistic values are shaded red, and negative values are shaded blue.  The greater the absolute value of the t-statistic, the greater the intensity (deeper shade) of the color.
@@ Line 389: / Line 389: @@
 The data was prepared for the t-test by
-# The BCell-100 data node was selected in the Project Folders component.  (It should have a child adjacency matrix from the CNKB "create network" step).
+# The BCell-100 data node was selected in the [[Workspace|Workspace]].  (It should have a child adjacency matrix from the CNKB "create network" step).
 # Normalization: threshold normalize to a minimum value of 1.0.
 # Normalization: log2 transform.
@@ Line 401: / Line 401: @@
 # log2-transformed data box: checked.
-After the t-test was calculated, the adjacency matrix  from the CNKB query (with parent BCell-100) was selected in the Project Folders component to redisplay the network in Cytoscape.
+After the t-test was calculated, the adjacency matrix  from the CNKB query (with parent BCell-100) was selected in the [[Workspace|Workspace]] to redisplay the network in Cytoscape.
 On the network display, the "Show t-test results" option was chosen.
@@ Line 432: / Line 432: @@
 ===Create subnetwork===
 The "Create subnetwork" feature intersects a network displayed in Cytoscape with a set of Markers defined in the Markers component.
-* A new adjacency matrix is created in the Project Folders component.  The new adjacency matrix is made a child of the same dataset as the network it was created from.
+* A new adjacency matrix is created in the [[Workspace|Workspace]].  The new adjacency matrix is made a child of the same dataset as the network it was created from.
 * The new subnetwork contains all nodes in the original network which are also in the selected marker set, regardless of whether they are connected by any edges.
@@ Line 439: / Line 439: @@
-After the new subnetwork is created, it is placed as a new Adjacency matrix in the Project Folders component.
+After the new subnetwork is created, it is placed as a new Adjacency matrix in the [[Workspace|Workspace]].
@@ Line 455: / Line 455: @@
-Note that creating a subnetwork actually creates a new adjacency matrix.  If you wish to return to the original adjacency matrix, select it in the Project Folders component.
+Note that creating a subnetwork actually creates a new adjacency matrix.  If you wish to return to the original adjacency matrix, select it in the [[Workspace|Workspace]].
 ===Compute Edge Correlations===
@@ Line 470: / Line 470: @@
 There are two possible ways in which the correlation value can be used:
-# To create a new subnetwork (represented by a new adjacency matrix in the Project Folders component) which contains only those edges (and the nodes they connect) which met the correlation threshold, or
+# To create a new subnetwork (represented by a new adjacency matrix in the [[Workspace|Workspace]]) which contains only those edges (and the nodes they connect) which met the correlation threshold, or
 # To display on the original network only those edges which which met the correlation threshold.  All nodes are still displayed.  (In this case, the sub-threshold edges are invisible but are still present).
@@ Line 529: / Line 529: @@
 This step can either be performed directly after the threshold has been set, or after the "Redraw network" command has been used.
-In either case, the subnetwork is represented by a newly created adjacency matrix in the Project Folders component.  This new network node is created as a child of the same microarray dataset from which it was derived.  Node attributes (like geneType) and edge attributes (like edge type) are copied over from the corresponding nodes and edges of the parent network.
+In either case, the subnetwork is represented by a newly created adjacency matrix in the [[Workspace|Workspace]].  This new network node is created as a child of the same microarray dataset from which it was derived.  Node attributes (like geneType) and edge attributes (like edge type) are copied over from the corresponding nodes and edges of the parent network.
-To return to the original network, select its adjacency matrix in the Project Folders component.
+To return to the original network, select its adjacency matrix in the [[Workspace|Workspace]].
 (Note that this diagram was created with an edited set of interaction-type colors).

← Older revision		Revision as of 17:24, 25 September 2013
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−	Similarly, colors are assigned to the lines (termed edges) connecting genes, which represent their interactions. These edges are colored based on the type of interaction, e.g. Protein-DNA etc.	+	Similarly, when molecular interaction types are available, colors are assigned to the lines (termed edges) connecting genes, which represent their interactions. These edges are colored based on the type of interaction, e.g. Protein-DNA etc.

	As currently implemented, colors are assigned randomly to each interaction type when geWorkbench starts up. There will thus be a different color palate with each invocation of geWorkbench. Within a single invocation of geWorkbench, the same color palate will be used for each network created.		As currently implemented, colors are assigned randomly to each interaction type when geWorkbench starts up. There will thus be a different color palate with each invocation of geWorkbench. Within a single invocation of geWorkbench, the same color palate will be used for each network created.

← Older revision		Revision as of 17:22, 25 September 2013
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−	When the molecular interaction type is available, edges are colored according to the interaction type, e.g. Protein-DNA. Molecular interation ~~type is~~ stored in the [[Cellular_Networks_KnowledgeBase\| Cellular Networks Knowledge Base (CNKB)]] and in SIF format network files, and are included when a network is created from either of those sources. The figure below shows the result of such a query against the CNKB.	+	When the molecular interaction type is available, edges are colored according to the interaction type, e.g. Protein-DNA. Molecular interation types are stored in the [[Cellular_Networks_KnowledgeBase\| Cellular Networks Knowledge Base (CNKB)]] and in SIF format network files, and are included when a network is created from either of those sources. The figure below shows the result of such a query against the CNKB.

← Older revision		Revision as of 17:21, 25 September 2013
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−	~~By default~~, edges are ~~now~~ colored according to the interaction type, e.g. Protein-DNA. ~~The figure below shows the result of a query carried out~~ in the [[Cellular_Networks_KnowledgeBase\| Cellular Networks Knowledge Base (CNKB)]] ~~chapter~~.	+	When the molecular interaction type is available, edges are colored according to the interaction type, e.g. Protein-DNA. Molecular interation type is stored in the [[Cellular_Networks_KnowledgeBase\| Cellular Networks Knowledge Base (CNKB)]] and in SIF format network files, and are included when a network is created from either of those sources. The figure below shows the result of such a query against the CNKB.

← Older revision		Revision as of 19:02, 16 July 2013
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−	[[Image:Cytoscape_correlation_subnetwork_displayed_log_v2.2.png]]	+	[[Image:Cytoscape_correlation_subnetwork_displayed_log_v2.2.png\|{{ImageMaxWidth}}]]

	====Reset network====		====Reset network====

← Older revision		Revision as of 19:02, 16 July 2013
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−	[[Image:Cytoscape_t-test_display_subnetwork_sig_created_v2.2.png]]	+	[[Image:Cytoscape_t-test_display_subnetwork_sig_created_v2.2.png\|{{ImageMaxWidth}}]]

	===Restore network===		===Restore network===

@@ Line 325: / Line 325: @@
-[[Image:CNKB_Cytoscape_Results_type_shapes_v2.2.png]]
+[[Image:CNKB_Cytoscape_Results_type_shapes_v2.2.png|{{ImageMaxWidth}}]]
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 [[Image:Cytoscape_VizMapper_EdgeColors_edit_v2.2.png]]
 ==Saving Changes to Network Attributes==

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 The figure below shows the result of applying the "Universe" style to a network where two nodes are selected (yellow).
-[[Image:Cytoscape_apply_visual_style_v2.2.png]]
+[[Image:Cytoscape_apply_visual_style_v2.2.png|{{ImageMaxWidth}}]]
 ==Edges colored by interaction type==

← Older revision		Revision as of 19:00, 16 July 2013
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−	[[Image:Cytoscape_2.8_Toolbar.png]]	+	[[Image:Cytoscape_2.8_Toolbar.png\|{{ImageMaxWidth}}]]