Difference between revisions of "Description of GenGIS plugins"

From The GenGIS wiki
Jump to: navigation, search
(Beta Diversity)
Line 15: Line 15:
 
=Bar Graph=
 
=Bar Graph=
  
Coming soon.
+
The ''Bar Graph'' plugin provides bar graphs showing the relative abundance of sequence data from two groups (Fig. 3). Groups can be defined be any field in your ''Location'' file and bar plots created for any numeric field in your ''Sequence'' file. You may optionally specify a ''Count field'' from the ''Sequence'' file indicates the number of times a given sequence is observed. This allows both qualitative and quantitative bar plots to be generated.
 +
 
 +
[[Image:BarGraphPlugin.png|thumb|center|600px|Figure 3. Bar Graph plugin.]]
  
 
=Beta Diversity=
 
=Beta Diversity=
  
The ''Beta Diversity'' plugin calculates [http://en.wikipedia.org/wiki/Beta_diversity beta diversity] between active locations (Fig. 3). The resulting biotic dissimilarity matrix can be saved to file and visualized in GenGIS using the ''Dissimilarity Matrix Viewer'' plugin. It currently calculate 9 measures of beta diversity (e.g., Bray-Curtis, Jaccard) across any field defined in your ''Sequence File''. Sequences classified as Other or Unclassified can be optionally ignored during the calculation of beta diversity. In order to account for unequal sampling depth, subsampling with replacement (i.e., jackknifing) can be performed and the mean beta-diversity between jackknifed samples reported. Hierarchical cluster trees indicating the relative similarity of locations can be produced and used as an input ''Tree File'' to GenGIS.  
+
The ''Beta Diversity'' plugin calculates [http://en.wikipedia.org/wiki/Beta_diversity beta diversity] between active locations (Fig. 4). The resulting biotic dissimilarity matrix can be saved to file and visualized in GenGIS using the ''Dissimilarity Matrix Viewer'' plugin. It currently calculate 9 measures of beta diversity (e.g., Bray-Curtis, Jaccard) across any field defined in your ''Sequence File''. Sequences classified as Other or Unclassified can be optionally ignored during the calculation of beta diversity. In order to account for unequal sampling depth, subsampling with replacement (i.e., jackknifing) can be performed and the mean beta-diversity between jackknifed samples reported. Hierarchical cluster trees indicating the relative similarity of locations can be produced and used as an input ''Tree File'' to GenGIS.  
  
[[Image:BetaDiversityPlugin.png‎|thumb|center|401px|Figure 3. Beta Diversity Plugin‎]]
+
[[Image:BetaDiversityPlugin.png‎|thumb|center|401px|Figure 4. Beta Diversity Plugin‎]]
  
 
=Dissimilarity Matrix Viewer=
 
=Dissimilarity Matrix Viewer=
Line 36: Line 38:
 
The first line indicates the number of locations and each of the following rows gives the dissimilarity values for the specified location. The location names (first column) must match those in your location file. The upper and lower triangles of the matrix can be different. For example, in this [[HIV-1 subtype B mobility in Europe | HIV-1 data set]], the two triangle indicate import and export rates.
 
The first line indicates the number of locations and each of the following rows gives the dissimilarity values for the specified location. The location names (first column) must match those in your location file. The upper and lower triangles of the matrix can be different. For example, in this [[HIV-1 subtype B mobility in Europe | HIV-1 data set]], the two triangle indicate import and export rates.
  
Elements in the matrix are selected by setting the ''Selection criteria'' (Fig. 4). Lines between the selected pairs are displayed in the ''Viewport'' using the specified ''Visual properties'' (Fig. 5). To update the ''Viewport'' display click ''Apply''.  
+
Elements in the matrix are selected by setting the ''Selection criteria'' (Fig. 5). Lines between the selected pairs are displayed in the ''Viewport'' using the specified ''Visual properties'' (Fig. 6). To update the ''Viewport'' display click ''Apply''.  
  
[[Image:DissimilarityMatrixViewer.png|thumb|center|600px|Figure 4. Dissimilarity Matrix Viewer plugin.]]
+
[[Image:DissimilarityMatrixViewer.png|thumb|center|600px|Figure 5. Dissimilarity Matrix Viewer plugin.]]
[[Image:DissimilarityMatrixViewport.png|thumb|center|322px|Figure 5. Display of all matrix elements between 5 and 10.]]
+
[[Image:DissimilarityMatrixViewport.png|thumb|center|322px|Figure 6. Display of all matrix elements between 5 and 10.]]
  
 
=Linear Regression=
 
=Linear Regression=
  
The ''Linear Regression'' plugin can be used to perform a linear regress between any two variables in the ''Location Table'' (see Location Table Viewer below). To perform the regression, the independent and dependent variables must be specified in the ''Regression analysis'' section of the plugin (Fig. 6). The results of the regression are reported within the plugin and shown as a scatter plot. A visualization within the GenGIS ''Viewport'' is also generated based on the properties set in the ''Viewport display'' section of the plugin (Fig. 7).  
+
The ''Linear Regression'' plugin can be used to perform a linear regress between any two variables in the ''Location Table'' (see Location Table Viewer below). To perform the regression, the independent and dependent variables must be specified in the ''Regression analysis'' section of the plugin (Fig. 7). The results of the regression are reported within the plugin and shown as a scatter plot. A visualization within the GenGIS ''Viewport'' is also generated based on the properties set in the ''Viewport display'' section of the plugin (Fig. 8).  
  
[[Image:LinearRegression.png|thumb|center|600px|Figure 6. Linear Regression plugin.]]
+
[[Image:LinearRegression.png|thumb|center|600px|Figure 7. Linear Regression plugin.]]
 
[[Image:LinearRegressionViewport.png|thumb|center|596px|Figure 7. Residuals of linear regression shown within the GenGIS Viewport.]]
 
[[Image:LinearRegressionViewport.png|thumb|center|596px|Figure 7. Residuals of linear regression shown within the GenGIS Viewport.]]
  
 
=Location Table Viewer=
 
=Location Table Viewer=
  
The ''Location Table Viewer'' plugin display a table indicating the metadata associated with each location (Fig. 8). 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.
+
The ''Location Table Viewer'' plugin display a table indicating the metadata associated with each location (Fig. 9). 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.
  
[[Image:LocationTable.png|thumb|center|600px|Figure 8. Location Table plugin.]]
+
[[Image:LocationTable.png|thumb|center|600px|Figure 9. Location Table plugin.]]
  
 
=Mantel=
 
=Mantel=
Line 60: Line 62:
 
The ''Mantel'' plugin can be used to perform a Mantel test between any two variables in the ''Location Table'' or ''Sequence Table''.
 
The ''Mantel'' plugin can be used to perform a Mantel test between any two variables in the ''Location Table'' or ''Sequence Table''.
  
[[Image:Mantel.png|thumb|center|600px|Figure 9. Mantel plugin.]]
+
[[Image:Mantel.png|thumb|center|600px|Figure 10. Mantel plugin.]]
  
 
=Multi-Tree Optimal-Crossing Test=
 
=Multi-Tree Optimal-Crossing Test=
  
[[Image:MultiTreeOptimalCrossingTest.png|thumb|center|600px|Figure 10. Multi-Tree Optimal-Crossing Test plugin.]]
+
[[Image:MultiTreeOptimalCrossingTest.png|thumb|center|600px|Figure 11. Multi-Tree Optimal-Crossing Test plugin.]]
  
 
=Sequence Table Viewer=
 
=Sequence Table Viewer=
  
The ''Sequence Table Viewer'' plugin display a table indicating the metadata associated with each sequence (Fig. 11). 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.  
+
The ''Sequence Table Viewer'' plugin display a table indicating the metadata associated with each sequence (Fig. 12). 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 11. Sequence Table plugin.]]
+
[[Image:SequenceTable.png|thumb|center|600px|Figure 12. Sequence Table plugin.]]

Revision as of 01:58, 5 April 2013

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.

Figure 1. Alpha Diversity plugin.

Alpha Diversity Visualizer

The Alpha Diversity Visualizer plugin can calculate alpha diversity for active locations, regress alpha diversity against location specific metadata, and produce visualizations of the resulting linear regression analysis. 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. 2). 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. Linear regression results of alpha diversity versus all numeric fields associated with locations are reported within the Linear Regression Results table. Selecting a row within this table causes a linear regression scatter plot of alpha diversity versus the selected Field to be generated. The Viewport Display section allows different Viewport visualization to be produced.

Figure 2. Alpha Diversity Visualizer plugin.

Bar Graph

The Bar Graph plugin provides bar graphs showing the relative abundance of sequence data from two groups (Fig. 3). Groups can be defined be any field in your Location file and bar plots created for any numeric field in your Sequence file. You may optionally specify a Count field from the Sequence file indicates the number of times a given sequence is observed. This allows both qualitative and quantitative bar plots to be generated.

File:BarGraphPlugin.png
Figure 3. Bar Graph plugin.

Beta Diversity

The Beta Diversity plugin calculates beta diversity between active locations (Fig. 4). The resulting biotic dissimilarity matrix can be saved to file and visualized in GenGIS using the Dissimilarity Matrix Viewer plugin. It currently calculate 9 measures of beta diversity (e.g., Bray-Curtis, Jaccard) across any field defined in your Sequence File. Sequences classified as Other or Unclassified can be optionally ignored during the calculation of beta diversity. In order to account for unequal sampling depth, subsampling with replacement (i.e., jackknifing) can be performed and the mean beta-diversity between jackknifed samples reported. Hierarchical cluster trees indicating the relative similarity of locations can be produced and used as an input Tree File to GenGIS.

Figure 4. Beta Diversity Plugin‎

Dissimilarity Matrix Viewer

The Dissimilarity Matrix Viewer plugin provides functionality for visualizing a matrix which indicates the dissimilarity between all pairs of locations. The dissimilarity matrix must be in the following format, where a \t indicates a tab:

 3
A\t0\t2\t3
B\t1\t0\t4
C\t3\t5\t0

The first line indicates the number of locations and each of the following rows gives the dissimilarity values for the specified location. The location names (first column) must match those in your location file. The upper and lower triangles of the matrix can be different. For example, in this HIV-1 data set, the two triangle indicate import and export rates.

Elements in the matrix are selected by setting the Selection criteria (Fig. 5). Lines between the selected pairs are displayed in the Viewport using the specified Visual properties (Fig. 6). To update the Viewport display click Apply.

Figure 5. Dissimilarity Matrix Viewer plugin.
Figure 6. Display of all matrix elements between 5 and 10.

Linear Regression

The Linear Regression plugin can be used to perform a linear regress between any two variables in the Location Table (see Location Table Viewer below). To perform the regression, the independent and dependent variables must be specified in the Regression analysis section of the plugin (Fig. 7). The results of the regression are reported within the plugin and shown as a scatter plot. A visualization within the GenGIS Viewport is also generated based on the properties set in the Viewport display section of the plugin (Fig. 8).

Figure 7. Linear Regression plugin.
Figure 7. Residuals of linear regression shown within the GenGIS Viewport.

Location Table Viewer

The Location Table Viewer plugin display a table indicating the metadata associated with each location (Fig. 9). 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.

Figure 9. Location Table plugin.

Mantel

  • Requirements: R with the ade4 library must be installed on your system (see the GenGIS manual).

The Mantel plugin can be used to perform a Mantel test between any two variables in the Location Table or Sequence Table.

Figure 10. Mantel plugin.

Multi-Tree Optimal-Crossing Test

Figure 11. Multi-Tree Optimal-Crossing Test plugin.

Sequence Table Viewer

The Sequence Table Viewer plugin display a table indicating the metadata associated with each sequence (Fig. 12). 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.

Figure 12. Sequence Table plugin.