User:Alex - Revision history

Alex: /* Creating Cartograms */

2017-05-12T00:58:04Z

Creating Cartograms

Alex: /* Loading Data */

2017-05-12T00:55:33Z

Loading Data

Alex at 00:54, 12 May 2017

2017-05-12T00:54:14Z

Alex at 00:51, 12 May 2017

2017-05-12T00:51:42Z

Alex: Created page with "=Introduction= GenGIS is a free and open-source bioinformatics application that allows geographic data to be merged with information about biological sequences collected from..."

2017-05-12T00:34:52Z

Created page with "=Introduction= GenGIS is a free and open-source bioinformatics application that allows geographic data to be merged with information about biological sequences collected from..."

New page

=Introduction=

GenGIS is a free and open-source bioinformatics application that allows geographic data to be merged with information about biological sequences collected from the environment. It consists of a 3D graphical user interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.

The ''Aneides lugubris'' of Western California, on of the top hotspots on the planet for species diversity where 33 of 44 salamander species are endemic to the state.

=Loading Data=

The Salamander data consists of a 2D map (Cali.tiff), location data (Aneides_Locations_Filtered.csv) and a phylogenetic tree (Aneides_Filtered.tre). For basic information on using the GenGIS interface and loading data please see the [[Katydid Tutorial | ''Banza'' Katydid Tutorial]].

=Changing Visual Properties=

The location set properties were selected to differentiate the data set my ''mtDNA clades''. The properties of the phylogenetic display were selected to ensure maximum visibility of locations on the map. For further details on setting visual properties see the [[Katydid Tutorial | ''Banza'' Katydid]] or [[GOS Tutorial | GOS]] tutorials.

=Creating Cartograms=

=Contact Information=

We encourage you to send us suggestions for new features. GenGIS is in active development and we are interested in discussing all potential applications of this software. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko@cs.dal.ca). If reporting a bug, please provide as much information as possible and, if possible, a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue.

=References=

← Older revision		Revision as of 00:58, 12 May 2017
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	In order to create a cartogram from a location set loaded in GenGIS you require as a basis a map and location set as a minimum. Sequence files can also be used as metadata to transform the map. By default the count of samples at each location is used to transform the map, which defaults to one per location if no Sequence file is loaded. To create a cartogram right click the map loaded map layer and select the ''Cartogram'' tab from the properties menu. To fine tune the cartogram two operations are available ''Location Radius'' and ''Variable Multiplier''. ''Location Radius'' adjusts the size of the grid cells the map is divided into when the cartogram is created. ''Variable Multiplier'' amplifies the value of populated grid cells by a X times multiple of the stored value. The ''Resize'' density option can also be used increase the run time of cartogram creation by decreasing the resolution by the specified percentage during creation time.		In order to create a cartogram from a location set loaded in GenGIS you require as a basis a map and location set as a minimum. Sequence files can also be used as metadata to transform the map. By default the count of samples at each location is used to transform the map, which defaults to one per location if no Sequence file is loaded. To create a cartogram right click the map loaded map layer and select the ''Cartogram'' tab from the properties menu. To fine tune the cartogram two operations are available ''Location Radius'' and ''Variable Multiplier''. ''Location Radius'' adjusts the size of the grid cells the map is divided into when the cartogram is created. ''Variable Multiplier'' amplifies the value of populated grid cells by a X times multiple of the stored value. The ''Resize'' density option can also be used increase the run time of cartogram creation by decreasing the resolution by the specified percentage during creation time.
		+
		+	[[Image:Aneides_l15_m15.png\|thumb\|center\|600px\|Figure 1. A cartogram created using ''Aneides lugubris'' and a Location Radius value of 15 and a Variable Multiplier of 5.]]

	=Contact Information=		=Contact Information=

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 The Salamander data consists of a 2D map (Cali.tiff), location data (Aneides_Locations_Filtered.csv) and a phylogenetic tree (Aneides_Filtered.tre). For basic information on using the GenGIS interface and loading data please see the [[Katydid Tutorial | ''Banza'' Katydid Tutorial]].
-[[Media:Aneides_Unstransformed.png|picture image]]
+[[Image:Aneides_Unstransformed.png|thumb|center|600px]]
 =Changing Visual Properties=

← Older revision		Revision as of 00:54, 12 May 2017
Line 8:		Line 8:

	The Salamander data consists of a 2D map (Cali.tiff), location data (Aneides_Locations_Filtered.csv) and a phylogenetic tree (Aneides_Filtered.tre). For basic information on using the GenGIS interface and loading data please see the [[Katydid Tutorial \| ''Banza'' Katydid Tutorial]].		The Salamander data consists of a 2D map (Cali.tiff), location data (Aneides_Locations_Filtered.csv) and a phylogenetic tree (Aneides_Filtered.tre). For basic information on using the GenGIS interface and loading data please see the [[Katydid Tutorial \| ''Banza'' Katydid Tutorial]].
		+	[[Media:Aneides_Unstransformed.png\|picture image]]

	=Changing Visual Properties=		=Changing Visual Properties=

@@ Line 15: / Line 15: @@
 =Creating Cartograms=
+In order to create a cartogram from a location set loaded in GenGIS you require as a basis a map and location set as a minimum. Sequence files can also be used as metadata to transform the map. By default the count of samples at each location is used to transform the map, which defaults to one per location if no Sequence file is loaded. To create a cartogram right click the map loaded map layer and select the ''Cartogram'' tab from the properties menu. To fine tune the cartogram two operations are available ''Location Radius'' and ''Variable Multiplier''. ''Location Radius'' adjusts the size of the grid cells the map is divided into when the cartogram is created. ''Variable Multiplier'' amplifies the value of populated grid cells by a X times multiple of the stored value. The ''Resize'' density option can also be used increase the run time of cartogram creation by decreasing the resolution by the specified percentage during creation time.
 =Contact Information=