The GenGIS Manual - Revision history

Timothy: /* Multiple identical sequences at a location */

2012-03-16T20:52:19Z

Multiple identical sequences at a location

Timothy: /* Sequence File */

2012-03-16T20:05:55Z

Sequence File

Timothy: /* Location File */

2012-03-16T20:05:10Z

Location File

Timothy: /* Multiple identical sequences at a location */

2012-03-16T17:08:39Z

Multiple identical sequences at a location

Timothy: /* RPy and analyzing data */

2012-03-16T17:06:26Z

RPy and analyzing data

Timothy: /* Graphical analysis tools in GenGIS */

2012-03-16T17:05:38Z

Graphical analysis tools in GenGIS

Timothy: /* Tree Layer Properties */

2012-03-16T17:04:05Z

Tree Layer Properties

Timothy: /* Interacting with sample sites */

2012-03-16T16:59:27Z

Interacting with sample sites

Timothy: /* Purpose */

2012-03-16T16:58:44Z

Purpose

Timothy: /* Purpose */

2012-03-16T16:56:52Z

Purpose

@@ Line 158: / Line 158: @@
 ====Multiple identical sequences at a location====
-A ''Count'' field may be specified to indicate the number of times a given sequence is present at a given site.  This has the benefit of significantly reducing the size of sequence files by eliminating the need to store multiple copies of identical sequences for each site.
+A ''count'' field may be specified within a Sequence File to indicate the number of times a given sequence is present at a given site.  This has the benefit of significantly reducing the size of a Sequence File.
-   Site Id,Sequence Id,Domain,Phylum,Class,Order,Family,Genus,Species,'''Count'''
+   Site Id, Sequence Id, '''Count''', Domain, Phylum, Class, Order, Family, Genus, Species
-The Count field, which can be assigned any custom name, must be correctly set within GenGIS through the Location Set Properties dialog:
+The ''count'' field can be assigned any name within the Sequence File. Multiple ''count'' fields may be specified indicating different quantitative aspects of a named sequence type such as number of sequences or total base pairs observed. The ''count'' field can then be specified in various locations within GenGIS. For example, quantitative pie charts reflecting the number of times each sequence type is observed at a location can be created through the Location Set Properties dialog:
 # Open the Location Set Properties dialog
@@ Line 168: / Line 168: @@
 # Select "Create quantitative charts using count data in field"
 # Select the desired count field from the adjacent drop down menu
 [[Image:V108 LocationSetProperties Charts ColourMap SettingCountField.PNG ]]

@@ Line 149: / Line 149: @@
 The '''first line''' of the file must begin with the following column headings:
-  Site ID, Sequence ID
+  Site ID,Sequence ID
 Columns containing custom information can be added after the two mandatory headings.  Each row of the sequence file must define a value for each of the columns identified in the header line.  Note that the 'sequence file' need not contain any molecular sequence data, nor do the entities necessarily need to have a one-to-one correspondence to actual sampled sequences.
@@ Line 155: / Line 155: @@
 A simple sequence file might summarize the taxonomic classification of each sampled sequence:
-  Site ID, Sequence ID, Best_match, Species, Genus, Family, Order, Class, Phylum, Superkingdom
+  Site ID,Sequence ID,Best_match,Species,Genus,Family,Order,Class,Phylum,Superkingdom
 ====Multiple identical sequences at a location====
 A ''Count'' field may be specified to indicate the number of times a given sequence is present at a given site.  This has the benefit of significantly reducing the size of sequence files by eliminating the need to store multiple copies of identical sequences for each site.
-   Site Id, Sequence Id, Domain, Phylum, Class, Order, Family, Genus, Species, '''Count'''
+   Site Id,Sequence Id,Domain,Phylum,Class,Order,Family,Genus,Species,'''Count'''
 The Count field, which can be assigned any custom name, must be correctly set within GenGIS through the Location Set Properties dialog:

@@ Line 126: / Line 126: @@
 The '''first line''' of the file may look something like the following:
-  Site ID, Latitude, Longitude
+  Site ID,Latitude,Longitude
 or
-  Site ID, Northing, Easting
+  Site ID,Northing,Easting
 depending on the coordinate system.
@@ Line 136: / Line 136: @@
 GenGIS provides the ability to specify many different custom column headers within the Location file, including longer descriptive site names, environmental parameters, or a time stamp.  For instance, a location file header might look like this:
-  Site ID, Latitude, Longitude, File Size, Environment Type, Geographic Location, Site Name, Country
+  Site ID,Latitude,Longitude,File Size,Environment Type,Geographic Location,Site Name,Country
 Each of these values '''must''' then be specified for every entity (= row in the file), even if they are called NULL or some other placeholder value.

@@ Line 162: / Line 162: @@
    Site Id, Sequence Id, Domain, Phylum, Class, Order, Family, Genus, Species, '''Count'''
-The Count field, which can be assigned any custom name, must be correctly set within GenGIS through the Location Set Properties dialog (see below).
+The Count field, which can be assigned any custom name, must be correctly set within GenGIS through the Location Set Properties dialog:
 # Open the Location Set Properties dialog

← Older revision		Revision as of 17:06, 16 March 2012
Line 849:		Line 849:

	By stitching together multiple key frames complex fly-through movies can be created. Commercial software such as [http://www.techsmith.com/camtasia.asp Camtasia] or open source software such as [http://sourceforge.net/projects/camstudio/ CamStudio] can be used to record these movies.		By stitching together multiple key frames complex fly-through movies can be created. Commercial software such as [http://www.techsmith.com/camtasia.asp Camtasia] or open source software such as [http://sourceforge.net/projects/camstudio/ CamStudio] can be used to record these movies.
−
−	~~=== RPy and analyzing data ===~~
−
−	~~<font color=red>'''Does this section need to be finished or can we remove it?'''</font>~~
−
−	~~==== Accessing sample data as tables in R ====~~
−
−	~~<font color=red>'''Does this section need to be finished or can we remove it?'''</font>~~
−
−	~~==== Capturing output from R ====~~
−
−	~~<font color=red>'''Does this section need to be finished or can we remove it?'''</font>~~

← Older revision		Revision as of 17:05, 16 March 2012
Line 688:		Line 688:
	\|}		\|}

−	~~== Graphical analysis tools in GenGIS ==~~

−	~~<font color=red>'''Does this section need to be finished or can we remove it?'''</font>~~
−
−	~~=== Basic data visualizations ===~~
−	~~==== Pie charts ====~~
−
−	~~=== 2D Trees ===~~
−
−	~~Coming soon!~~
−
−	The algorithm to layout a 2D tree has an exponential running time in the degree of a node. As such, we do not suggest trying to layout trees with nodes of degree > 10. Details of this algorithm are given in:
−
−	~~Parks, D.H. and Beiko, R.G. (2009). Quantitative visualizations of hierarchically organized data in a geographic context. Accepted to Geoinformatics 2009, Fairfax, VA.~~
−
−	~~==== Defining axes ====~~
−	~~==== Manipulation ====~~
−
−	~~=== 3D Trees ===~~

	== The Python console and API functions ==		== The Python console and API functions ==

@@ Line 627: / Line 627: @@
 === Tree Layer Properties ===
-GenGIS supports 2D and 3D trees.  Different display properties (e.g., colour, line width) can be assigned to trees through the Tree Layer Properties dialog.  GenGIS supports loading multiple trees during a single session.  Components of the Tree Layer properties dialog are explained in greater detail below.
+GenGIS supports 2D and 3D trees (e.g., phylogenetic or hierarchical cluster tree).  Different display properties (e.g., colour, line width) can be assigned to trees through the Tree Layer Properties dialog.  GenGIS supports loading multiple trees during a single session.  Components of the Tree Layer properties dialog are explained in greater detail below.
 {| cellpadding="10%" cellspacing="0" style="border:1px solid #BBB"

← Older revision		Revision as of 16:59, 16 March 2012
Line 340:		Line 340:
	[[Image:V108_PythonConsole.png\|frame\|none\|The GenGIS Python console.]]		[[Image:V108_PythonConsole.png\|frame\|none\|The GenGIS Python console.]]

−	~~=== Interacting with sample sites ===~~

−	~~<font color=red>'''Does this section need to be finished or can we remove it?'''</font>~~

	== Layer Property Dialogs ==		== Layer Property Dialogs ==

@@ Line 15: / Line 15: @@
 ; User-Friendly Interface
-: Although GenGIS is built to deal with challenging scientific questions, our goal is to make the software as easy to use as possible. This is particularly important as many users will have little experience with digital map data, apart from applications such as Google Earth.
+: Although GenGIS is built to deal with challenging scientific questions, our goal is to make the software easy to use. This is particularly important as many users will have little experience with digital map data, apart from applications such as Google Earth.
 ; Adaptible and Extensible

@@ Line 7: / Line 7: @@
 Geography has always been an important component of evolutionary and ecological theory.  The advent of sequence typing approaches such as 16S ribotyping, DNA barcoding using the COX1 gene, and multi-locus sequence typing, gives us the opportunity to understand how communities of organisms interact, disperse and evolve.  This sequencing revolution is tightly coupled to the development of new algorithms for assessing and comparing populations based on their genes.
-Coupled with these developments is the ready availability of high quality, public domain digital map data.  By integrating molecular data with cartography and habitat parameters, we can visualize the geographic and ecological factors that influence community composition and function.
+Coupled with these developments is the availability of high quality, public domain digital map data.  By integrating molecular data with cartography and habitat parameters, we can visualize the geographic and ecological factors that influence community composition and function.
 GenGIS is designed to bring these components together into a single software package that satisfies the following criteria: