Hierarchical Clustering - Revision history

Smith: /* Overview */

2015-03-19T21:39:00Z

‎Overview

2014-01-22T22:27:07Z

‎Left-click actions

2014-01-22T22:15:39Z

‎Set Selection

2014-01-22T22:14:18Z

‎Clustering Dimension

2014-01-22T22:12:13Z

‎Overview

2014-01-22T22:09:26Z

‎Working with a subtree in the Dendrogram

2014-01-22T22:08:34Z

‎Right-click menu items

2014-01-22T22:07:54Z

‎Bulb Icon

2014-01-22T22:03:57Z

‎Working with a subtree in the Dendrogram

2014-01-22T22:03:19Z

‎Working with Hierarchical Clustering Results

← Older revision		Revision as of 21:39, 19 March 2015
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	==Overview==		==Overview==
		+	For the '''geWorkbench web''' version of Hierarchical Clustering please see [[Hierarchical_Clustering_web]].
		+
		+
	Hierarchical clustering is a method to group arrays and/or markers together based on similarity of their expression profiles.		Hierarchical clustering is a method to group arrays and/or markers together based on similarity of their expression profiles.

← Older revision		Revision as of 22:27, 22 January 2014
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	[[Image:HC_Dendrogram_Tooltip.png]]		[[Image:HC_Dendrogram_Tooltip.png]]
−
−	~~===Left-click actions===~~
−	~~Left clicking on any point on the dendrogram will highlight the selected marker in the Markers component.~~

	===Right-click menu items===		===Right-click menu items===

@@ Line 60: / Line 60: @@
 ===Set Selection===
-Most geWorkbench analysis components provide the "All Arrays" and "All Markers" check-boxes to allow any activated sets of arrays or markers to be overridden.  Normally, activating one or more sets of markers or arrays limits an analysis to those items in the active set(s).
+Activating one or more sets of markers or arrays in the [[Marker_Sets]] or [[Array_Sets]] components limits an analysis to those items in the active set(s).
 ==Analysis Actions==

@@ Line 46: / Line 46: @@
 These are used to indicate whether to cluster markers, microarrays, or both.
-* '''Marker''' - Cluster the selected markers (genes) only based on the similarity across microarrays.
+* '''Marker''' - Cluster the selected markers (genes) based on the similarity across microarrays.
-* '''Microarray''' - Cluster the selected microarrays only based on the similarity across markers.
+* '''Microarray''' - Cluster the selected microarrays based on the similarity across markers.
 * '''Both''' - Cluster both markers and microarrays.

@@ Line 3: / Line 3: @@
 ==Overview==
-Hierarchical clustering is a method to group arrays and/or markers together based on similarity on their expression profiles.
+Hierarchical clustering is a method to group arrays and/or markers together based on similarity of their expression profiles.
 geWorkbench implements its own code for agglomerative hierarchical clustering.  Starting from individual points (the leaves of the tree), nearest neighbors are found for individual points, and then for groups of points, at each step building up a branched structure that converges toward a root that contains all points.  The resulting graph tends to group similar items together.

← Older revision		Revision as of 22:09, 22 January 2014
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−	[[Image:~~T_HC_Dendrogram_add-to-set~~.png]]	+	[[Image:HC_Dendrogram_add_to_set.png]]

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 * '''Add to Set''' - add the markers represented in the currently displayed tree to a new set in the Markers component called "Cluster Tree".  This is most useful if done after a subtree of markers has been selected.
-[[Image:T_HC_Dendrogram_add-to-set.png]]
+[[Image:HC_Dendrogram_add_to_set.png]]
 ==Working with Hierarchical Clustering Results==

@@ Line 139: / Line 139: @@
 * Signal: the expression value of the selected marker on the selected array.
-[[Image:T_Color_Mosaic_Tooltip.png]]
+[[Image:HC_Dendrogram_Tooltip.png]]
 ===Left-click actions===

← Older revision		Revision as of 22:03, 22 January 2014
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−	Arrays are added to the Arrays component, as shown here:	+	Arrays are added to the Arrays component (labeled "Cluster Tree [10]"), as shown here:


	[[Image:HC_Array_ClusterTree.png]]		[[Image:HC_Array_ClusterTree.png]]

@@ Line 156: / Line 156: @@
 ==Working with Hierarchical Clustering Results==
-The following figure show a close-up of the dendrogram produced by the above hierarchical clustering example.  The four horizontal bars shown in the diagram were added just to show the boundaries of the four array sets used.  (Note - you do not need to activate sets for clustering, unless you wish to use only a subset of all available arrays or markers).
+===Selecting a subtree===
-===Selecting a subtree===
+[[Image:HierarchicalClustering_Dendrogram_select_markers.png|{{ImageMaxWidth}}]]
 ===Working with a subtree in the Dendrogram===
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-The following figure shows the the new set of markers (labeled "Cluster Tree [17]") after it has been added to the Markers component.  The number in brackets indications how many markers are contained in the set.
+The following figure shows the the new set of markers (labeled "Cluster Tree [105]") after it has been added to the Markers component.  The number in brackets indications how many markers are contained in the set.
-[[Image:T_HC_ArraySets-ClusterTree.png]]
+[[Image:HC_Array_ClusterTree.png]]