Difference between revisions of "Description of GenGIS plugins"
| Line 9: | Line 9: | ||
=Alpha Diversity Visualizer= | =Alpha Diversity Visualizer= | ||
| + | [[Image:AlphaDiversityCalculator.png|thumb|center|600px|Figure 2. Alpha Diversity Visualizer plugin.]] | ||
| + | =Dissimilarity Matrix Viewer= | ||
| − | + | [[Image:DissimilarityMatrixViewer.png|thumb|center|600px|Figure 3. Dissimilarity Matrix Viewer plugin.]] | |
=Linear Regression= | =Linear Regression= | ||
| + | |||
| + | [[Image:LinearRegression.png|thumb|center|600px|Figure 4. Linear Regression plugin.]] | ||
=Location Table Viewer= | =Location Table Viewer= | ||
| Line 22: | Line 26: | ||
=Mantel= | =Mantel= | ||
| + | |||
| + | [[Image:Mantel.png|thumb|center|600px|Figure 7. Mantel plugin.]] | ||
=Sequence Table Viewer= | =Sequence Table Viewer= | ||
| − | The ''Sequence Table Viewer'' plugin display a table indicating the metadata associated with each sequence (Fig. | + | The ''Sequence Table Viewer'' plugin display a table indicating the metadata associated with each sequence (Fig. 8). Other plugins and custom Python scripts can be used to add data to the ''Sequence Table''. By default, only data for active locations and active sequences is shown. To show data for all locations check the ''Show data for all locations'' checkbox. To show data for all sequences check the ''Show data for all sequences'' checkbox. |
| − | [[Image:SequenceTable.png|thumb|center|600px|Figure | + | [[Image:SequenceTable.png|thumb|center|600px|Figure 8. Sequence Table plugin.]] |
Revision as of 15:25, 4 March 2012
GenGIS provides the following Python plugins which can be accessed through the Plugins menu.
Contents
Alpha Diversity
The Alpha Diversity plugin calculates alpha diversity for active locations. It currently calculate richness, Shannon, and Simpson alpha diversity. To calculate alpha diversity, you must select the Measure you wish to calculate and the Category field in your sequence file over which diversity will be calculate (Fig. 1). You may optionally select a Count field which indicates the number of times a given sequence is observed at a location. Pressing Calculate causes alpha diversity to be calculated. Results are reported within the plugin and added to the location table for use within GenGIS and other plugins.
Alpha Diversity Visualizer
Dissimilarity Matrix Viewer
Linear Regression
Location Table Viewer
The Location Table Viewer plugin display a table indicating the metadata associated with each location (Fig. 6). Other plugins and custom Python scripts can be used to add data to the Location Table. By default, only data for active locations is shown. To show data for all locations check the Show data for all locations checkbox.
Mantel
Sequence Table Viewer
The Sequence Table Viewer plugin display a table indicating the metadata associated with each sequence (Fig. 8). Other plugins and custom Python scripts can be used to add data to the Sequence Table. By default, only data for active locations and active sequences is shown. To show data for all locations check the Show data for all locations checkbox. To show data for all sequences check the Show data for all sequences checkbox.
