Description of GenGIS plugins - Revision history

Alex: /* Geographically Coupled Phylogenetic Distance (GCPD) */

2016-05-15T20:37:26Z

Geographically Coupled Phylogenetic Distance (GCPD)

Alex: /* Geographically Coupled Phylogenetic Distance (GCPD) */

2016-05-15T17:08:03Z

Geographically Coupled Phylogenetic Distance (GCPD)

Alex: /* Geographically Coupled Phylogenetic Distance (GCPD) */

2016-05-15T17:07:25Z

Geographically Coupled Phylogenetic Distance (GCPD)

Alex at 17:07, 15 May 2016

2016-05-15T17:07:05Z

Alex: /* Show Spread */

2014-06-18T16:54:12Z

Show Spread

Alex: /* Show Spread */

2014-06-18T16:51:04Z

Show Spread

Alex: /* Show Spread */

2014-06-18T16:48:58Z

Show Spread

Beiko at 01:20, 15 June 2014

2014-06-15T01:20:29Z

Alex: /* Step 1: The Query */

2013-12-12T19:34:23Z

Step 1: The Query

Alex: /* Step 1: The Query */

2013-12-12T19:32:58Z

Step 1: The Query

← Older revision		Revision as of 20:37, 15 May 2016
Line 197:		Line 197:

	The ''Geographically Coupled Phylogenetic Distance'' or ''GCPD'' plugin calculates the phylogenetic distance between samples at associated with locations. This calculation occurs in two steps, first the construction of a geographic scaffold, second a distribution of phylogenetic distances through this scaffold. To calculate ''GCPD'' you must select have a location layer and tree layer. A sequence layer is only required if the phylogenetic tree resolves to this layer. To run the ''GCPD'' plugin you must select a location layer for the distortion and a tree layer associated with it, as well as a method of normalization. Phylogenetic weighting can also be selected, taking either phylogenetic distance or it's reverse, in order to calculate how closely or distantly two samples are related respectively. Once these parameters have been sent the ''Calculate'' button can be used to begin the ''GCPD'' process. Once values have been calculated they can be added to the selected location layer using the ''Add To GenGIS'' button.		The ''Geographically Coupled Phylogenetic Distance'' or ''GCPD'' plugin calculates the phylogenetic distance between samples at associated with locations. This calculation occurs in two steps, first the construction of a geographic scaffold, second a distribution of phylogenetic distances through this scaffold. To calculate ''GCPD'' you must select have a location layer and tree layer. A sequence layer is only required if the phylogenetic tree resolves to this layer. To run the ''GCPD'' plugin you must select a location layer for the distortion and a tree layer associated with it, as well as a method of normalization. Phylogenetic weighting can also be selected, taking either phylogenetic distance or it's reverse, in order to calculate how closely or distantly two samples are related respectively. Once these parameters have been sent the ''Calculate'' button can be used to begin the ''GCPD'' process. Once values have been calculated they can be added to the selected location layer using the ''Add To GenGIS'' button.
		+
		+	GCPD can be used in cartogram creation [http://kiwi.cs.dal.ca/GenGIS/The_GenGIS_2.5_Manual#Creating_a_Cartogram], in order to visualize the role geography may play in phylogenetic distribution.

	[[Image:gcpd1.png\|thumb\|center\|600px\|GCPD plugin.]]		[[Image:gcpd1.png\|thumb\|center\|600px\|GCPD plugin.]]

@@ Line 198: / Line 198: @@
 The ''Geographically Coupled Phylogenetic Distance'' or ''GCPD'' plugin calculates the phylogenetic distance between samples at associated with locations. This calculation occurs in two steps, first the construction of a geographic scaffold, second a distribution of phylogenetic distances through this scaffold. To calculate ''GCPD'' you must select have a location layer and tree layer. A sequence layer is only required if the phylogenetic tree resolves to this layer. To run the ''GCPD'' plugin you must select a location layer for the distortion and a tree layer associated with it, as well as a method of normalization. Phylogenetic weighting can also be selected, taking either phylogenetic distance or it's reverse, in order to calculate how closely or distantly two samples are related respectively. Once these parameters have been sent the ''Calculate'' button can be used to begin the ''GCPD'' process. Once values have been calculated they can be added to the selected location layer using the ''Add To GenGIS'' button.
-[[Image::gcpd1.png|thumb|center|600px|GCPD plugin.]]
+[[Image:gcpd1.png|thumb|center|600px|GCPD plugin.]]
 ==Linear Regression==

@@ Line 198: / Line 198: @@
 The ''Geographically Coupled Phylogenetic Distance'' or ''GCPD'' plugin calculates the phylogenetic distance between samples at associated with locations. This calculation occurs in two steps, first the construction of a geographic scaffold, second a distribution of phylogenetic distances through this scaffold. To calculate ''GCPD'' you must select have a location layer and tree layer. A sequence layer is only required if the phylogenetic tree resolves to this layer. To run the ''GCPD'' plugin you must select a location layer for the distortion and a tree layer associated with it, as well as a method of normalization. Phylogenetic weighting can also be selected, taking either phylogenetic distance or it's reverse, in order to calculate how closely or distantly two samples are related respectively. Once these parameters have been sent the ''Calculate'' button can be used to begin the ''GCPD'' process. Once values have been calculated they can be added to the selected location layer using the ''Add To GenGIS'' button.
-[[Image::Gcpd1.png|thumb|center|600px|GCPD plugin.]]
+[[Image::gcpd1.png|thumb|center|600px|GCPD plugin.]]
 ==Linear Regression==

← Older revision		Revision as of 17:07, 15 May 2016
Line 193:		Line 193:

	[[Image:EnvBarPlots.jpg\|thumb\|center\|600px\|Map showing bar graph and color gradient representation of site pH.]]		[[Image:EnvBarPlots.jpg\|thumb\|center\|600px\|Map showing bar graph and color gradient representation of site pH.]]
		+
		+	==Geographically Coupled Phylogenetic Distance (GCPD)==
		+
		+	The ''Geographically Coupled Phylogenetic Distance'' or ''GCPD'' plugin calculates the phylogenetic distance between samples at associated with locations. This calculation occurs in two steps, first the construction of a geographic scaffold, second a distribution of phylogenetic distances through this scaffold. To calculate ''GCPD'' you must select have a location layer and tree layer. A sequence layer is only required if the phylogenetic tree resolves to this layer. To run the ''GCPD'' plugin you must select a location layer for the distortion and a tree layer associated with it, as well as a method of normalization. Phylogenetic weighting can also be selected, taking either phylogenetic distance or it's reverse, in order to calculate how closely or distantly two samples are related respectively. Once these parameters have been sent the ''Calculate'' button can be used to begin the ''GCPD'' process. Once values have been calculated they can be added to the selected location layer using the ''Add To GenGIS'' button.
		+
		+	[[Image::Gcpd1.png\|thumb\|center\|600px\|GCPD plugin.]]

	==Linear Regression==		==Linear Regression==

@@ Line 250: / Line 250: @@
 The ''Show Spread'' plugin allows subsets of location and sequence data to be visualized by stepping through any data field, either cumulatively or subset-by-subset. The user is required to provide a base map and location file as a minimum. Show Spread can also add branches to a geophylogeny as entities appear (and disappear).
-[[Image:defaultView.png|thumb|center|401px|Show Spread Default View.]]
-[[Image:advancedView.png|thumb|center|401px|Show Spread Advanced View.]]
+{| cellpadding="10%" cellspacing="0" style="border:1px solid #BBB"
 ===Default Components===

← Older revision		Revision as of 01:20, 15 June 2014
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	[[Image:RCA_plugin.png\|thumb\|center\|600px\|Reference Condition Analysis plugin.]]		[[Image:RCA_plugin.png\|thumb\|center\|600px\|Reference Condition Analysis plugin.]]
		+
		+	==Show Spread==
		+
		+	The ''Show Spread'' plugin allows subsets of location and sequence data to be visualized by stepping through any data field, either cumulatively or subset-by-subset. The user is required to provide a base map and location file as a minimum. Show Spread can also add branches to a geophylogeny as entities appear (and disappear).
		+
		+	[[Image:Basic.png\|thumb\|center\|401px\|Show Spread.]]
		+
		+	===Default Components===
		+
		+	Data: The data field to be iterated over by Show Spread. Only activated location fields will be used.
		+
		+	Sort: Visualize data in descending or ascending order.
		+
		+	Start: The starting point for the iteration.
		+
		+	Stop: The stopping point for the iteration.
		+
		+	Number of Steps: The number of divisions to be made in the data between the start and stop points.
		+
		+	Time per Step: The length of each step in tenths of a second.
		+
		+	OK: Run Show Spread.
		+
		+	Close: Close Show Spread.
		+
		+	?: Access the Help page for Show Spread.
		+
		+	===Advanced Components===
		+
		+	Colour by Intensity: Recolour locations based on the number of sequences displayed.
		+
		+	Binning: Display individual bins rather than cumulative data. Bin size will have to be defined.
		+
		+	Step Size: The size of a step taken by each increment of Show Spread.
		+
		+	Bin Start: The lower boundary (distance) for data to be considered inside a discrete bin.
		+
		+	Bin End: The upper boundary (distance) for data to be considered inside a discrete bin.
		+
		+	D/M/Y vs. M/D/Y: Whether dates used to define bins are to be interpreted as Day/Month/Year or Month/Day/Year.
		+
		+	Restore: Restores the size and colour of locations to their state previous to running Show Spread.

@@ Line 55: / Line 55: @@
 ===Step 1: The Query===
-The ''MG-RAST Query'' plugin can search MG-RAST for studies based upon organism name or function. This can be selected from the ''Options'' button highlighted below.
+The ''MG-RAST Query'' plugin can search MG-RAST for studies based upon organism name or function. Alternatively, studies can be retrieved directly by searching the corresponding ID. This can be selected from the ''Options'' button highlighted below.
 [[Image:mgrast1.png|thumb|center|600px|MG-Rast Plugin.]]