GeWorkbench-web/Set View - Revision history

Smith: moved GeWorkbench-web Set View to GeWorkbench-web/Set View

2015-04-27T18:46:55Z

moved GeWorkbench-web Set View to GeWorkbench-web/Set View

Smith at 22:30, 27 March 2015

2015-03-27T22:30:52Z

Smith: /* Markers and Arrays */

2015-03-23T16:36:12Z

‎Markers and Arrays

Smith: /* Overview */

2015-03-23T16:34:59Z

‎Overview

Smith: /* Set View */

2015-03-23T16:34:24Z

‎Set View

Smith: /* Markers and Arrays */

2015-03-23T15:48:43Z

‎Markers and Arrays

Smith: /* Markers and Arrays */

2015-03-23T15:47:57Z

‎Markers and Arrays

Smith: /* Main Menu Items */

2015-03-23T15:46:47Z

‎Main Menu Items

Smith at 03:34, 23 March 2015

2015-03-23T03:34:01Z

Smith: Created page with "==Set View== The picture below shows the "Set View". Sets of arrays or markers can be created in geWorkbench or uploaded from a file. ==Main Menu Items== [[Image:Workspace_we..."

2015-03-23T03:25:35Z

Created page with "==Set View== The picture below shows the "Set View". Sets of arrays or markers can be created in geWorkbench or uploaded from a file. ==Main Menu Items== [[Image:Workspace_we..."

New page

==Set View==

The picture below shows the "Set View". Sets of arrays or markers can be created in geWorkbench or uploaded from a file.

==Main Menu Items==

[[Image:Workspace_web_set_view.png]]

* Workspace View - switch back to the Workspace
* "x" - delete the currently selected item
* "up arrow" - upload a file containing a list of markers or arrays, one item per line
* "down arrow" - download a marker or array set to a file.

===A note about Contexts===
geWorkbench provides the ability to maintain multiple collections or "contexts" of marker or array sets. These can be used to group the data in various ways. However, there is no limit on the number of sets that can be created even in the default context, so the use of contexts is entirely optional.

===Markers and Arrays===
Markers and Arrays have the same actions. The following images use markers and marker dets to illustrate the functions, but they apply equally to arrays and array sets.

* Context for Marker Sets or Array Sets/Phenotypes
** Pulldown list including the "Default Context" as well as any user-created sets.
** '''New''' - Create a new context
* Markers or Arrays - An expandable list of of all markers / arrays part of the current expression dataset
* Marker / Array Sets - An expandable list of all marker / array sets for the current expression dataset.
* Marker / Array sets can be
** created as the result of e.g. an ANOVA or t-test analysis (for markers) or hierarchical clustering (arrays) producing a resulting set of markers or arrays
** uploaded from a file, or
** created manually in the Markers or Arrays list

The below image shows a single marker set created as the result of running an ANOVA analysis. It also shows sets of arrays created in an array context "Class".

[[Image:Workspace_web_set_view_opened.png]]

In the Markers or Arrays list, right-clicking produces a pop-up menu with these options:
* Add Set - Add selected (highlighted) markers or arrays to a new set. You will be prompted to enter a name.
* Filter - A text input will appear that allows filtering the list to show only markers /arrays containing the entered text. The match can be anywhere in a name.
* Remove Filter - Undo the filtering action and display the entire list again.

[[Image:Workspace_web_set_view_options.png]]

The following images show the result of selecting "Filter" in the Markers list,

[[Image:Workspace_web_set_view_filter.png]]

and then entering the text string "mapk", so that only markers with "mapk" in their names are displayed:

[[Image:Workspace_web_set_view_filter_mapk.png]]

Some or all of the markers can now be selected and the list right-clicked on again. Choosing "Add Set" will bring up the dialog "Add Markers to Set" in which a new set name can be entered:

[[Image:Workspace_web_set_view_add_to_set.png]]

The new set is then seen in the "Marker Sets" list with the number indicating it has 32 markers (red arrow).

[[Image:Workspace_web_set_view_new_set.png]]

If a set is clicked on, it has a single option:
* Rename - rename the set

The same actions can be performed on the Arrays list

← Older revision		Revision as of 22:30, 27 March 2015
Line 1:		Line 1:
−	{{~~TutorialsTopNav~~}}	+	{{Template:GeWorkbench-webTutorialsTopNav}}

@@ Line 24: / Line 24: @@
 ** '''New''' - Create a new context
 * '''Markers''' or '''Arrays''' - An expandable list of of all markers / arrays part of the current expression dataset
-* '''Marker Sets''' / '''Array Sets''' - An expandable list of all marker sets / array sets for the current expression dataset.
+* '''Marker Sets''' / '''Array Sets''' - An expandable list of all marker sets / array sets for the current expression dataset.  Marker Sets / Array Sets can be
 ** created as the result of e.g. an ANOVA or t-test analysis (for markers) or hierarchical clustering (arrays) producing a resulting set of markers or arrays
 ** uploaded from a file, or

@@ Line 3: / Line 3: @@
 ==Overview==
-Sets of arrays or markers can be created in geWorkbench or uploaded from a file.  They can also be created directly in the graphical interface, and can also be the output of analysis routines or created within visualization modules.
+Sets of arrays or markers can be created in geWorkbench or uploaded from a file.  They can also be the output of analysis routines or created within visualization modules.
 ==Main Menu Items==

@@ Line 2: / Line 2: @@
-==Set View==
+==Overview==
+Sets of arrays or markers can be created in geWorkbench or uploaded from a file.  They can also be created directly in the graphical interface, and can also be the output of analysis routines or created within visualization modules.
 ==Main Menu Items==

← Older revision		Revision as of 03:34, 23 March 2015
Line 1:		Line 1:
		+	{{TutorialsTopNav}}
		+
		+
	==Set View==		==Set View==

← Older revision	Revision as of 18:46, 27 April 2015
(No difference)

@@ Line 21: / Line 21: @@
 Markers and Arrays have the same actions.  The following images use markers and marker dets to illustrate the functions, but they apply equally to arrays and array sets.
-* Context for Marker Sets or Array Sets/Phenotypes
+* '''Context''' for Marker Sets or Array Sets/Phenotypes
 ** Pulldown list including the "Default Context" as well as any user-created sets.
 ** '''New''' - Create a new context
-* Markers or Arrays - An expandable list of of all markers / arrays part of the current expression dataset
+* '''Markers''' or '''Arrays''' - An expandable list of of all markers / arrays part of the current expression dataset
-* Marker Sets / Array Sets - An expandable list of all marker sets / array sets for the current expression dataset.
+* '''Marker Sets''' / '''Array Sets''' - An expandable list of all marker sets / array sets for the current expression dataset.
 * Marker Sets / Array Sets can be
 ** created as the result of e.g. an ANOVA or t-test analysis (for markers) or hierarchical clustering (arrays) producing a resulting set of markers or arrays

@@ Line 10: / Line 10: @@
 [[Image:Workspace_web_set_view.png]]
-* Workspace View - switch back to the Workspace
+* '''Workspace View''' - switch back to the [[GeWorkbench-web_Overview|Workspace]]
-* "x" - delete the currently selected item
+* "'''x'''" - delete the currently selected item
-* "up arrow" - upload a file containing a list of markers or arrays, one item per line
+* "'''up arrow'''" - upload a file containing a list of markers or arrays, one item per line
-* "down arrow" - download a marker or array set to a file.
+* "'''down arrow'''" - download a marker or array set to a file.
 ===A note about Contexts===
@@ Line 38: / Line 38: @@
 In the Markers or Arrays list, right-clicking produces a pop-up menu with these options:
-* Add Set - Add selected (highlighted) markers or arrays to a new set.  You will be prompted to enter a name.
+* '''Add Set''' - Add selected (highlighted) markers or arrays to a new set.  You will be prompted to enter a name.
-* Filter - A text input will appear that allows filtering the list to show only markers /arrays containing the entered text.  The match can be anywhere in a name.
+* '''Filter''' - A text input will appear that allows filtering the list to show only markers /arrays containing the entered text.  The match can be anywhere in a name.
-* Remove Filter - Undo the filtering action and display the entire list again.
+* '''Remove Filter''' - Undo the filtering action and display the entire list again.
 [[Image:Workspace_web_set_view_options.png]]
@@ Line 65: / Line 65: @@
 If a set is clicked on, it has a single option:
-* Rename - rename the set
+* '''Rename''' - rename the set
 The same actions can be performed on the Arrays list