Katydid Tutorial - Revision history

Dparks: /* References */

2012-03-02T21:08:07Z

References

Dparks: /* Quantitative Analysis of Geographic Structure */

2012-03-02T21:06:14Z

Quantitative Analysis of Geographic Structure

Dparks: /* Quantitative Analysis of Geographic Structure */

2012-03-02T19:38:34Z

Quantitative Analysis of Geographic Structure

Dparks: /* Introduction */

2012-03-02T19:11:07Z

Introduction

Dparks: /* Making Movies */

2012-03-02T18:04:00Z

Making Movies

Dparks: /* Tree Properties */

2012-03-02T17:59:09Z

Tree Properties

Dparks: /* References */

2012-03-02T17:44:12Z

References

Dparks: /* References */

2012-03-02T13:10:25Z

References

Dparks: /* Tree Properties */

2012-03-01T22:18:32Z

Tree Properties

Dparks: /* Map Properties */

2012-03-01T22:18:06Z

Map Properties

← Older revision		Revision as of 21:08, 2 March 2012
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	=References=		=References=
		+	Parks DH and Beiko RG. 2009. Quantitative Visualizations of Hierarchically Organized Data in a Geographic Context. ''27th International Conference on Geoinformatics'', Fairfax, Virgina. [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&isnumber=5292806&arnumber=5293552&count=243&index=6 IEEE Xplore]
		+
		+	Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S and Beiko RG. 2009. GenGIS: A geospatial information system for genomic data. ''Genome Research'', '''19''': 1896-1904.
		+
	Shapiro LH, Strazanac JS, and Roderick GK. 2006. Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago. ''Mol. Phylogenet. Evol.'' '''41''':53-63. [http://www.ncbi.nlm.nih.gov/pubmed/16781170 Pubmed]		Shapiro LH, Strazanac JS, and Roderick GK. 2006. Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago. ''Mol. Phylogenet. Evol.'' '''41''':53-63. [http://www.ncbi.nlm.nih.gov/pubmed/16781170 Pubmed]
−
−	Parks DH and Beiko RG. 2009. Quantitative Visualizations of Hierarchically Organized Data in a Geographic Context. ''27th International Conference on Geoinformatics'', Fairfax, Virgina. [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&isnumber=5292806&arnumber=5293552&count=243&index=6 IEEE Xplore]

@@ Line 65: / Line 65: @@
 =Quantitative Analysis of Geographic Structure=
-The 3D geophylogeny illustrated in Figure 9 provides strong qualitative evidence that geography has had a substantial influence on the evolution of ''Banza'' katydids. GenGIS also allows a quantitative analysis of the role of geography to be performed. This is done by drawing a 2D geophylogeny where the leaf nodes are ordered such that they maximize the goodness-of-fit between the tree and geography (Parks and Beiko, 2009). To perform this analysis follow these steps:
+The 3D geophylogeny illustrated in Figure 9 provides strong qualitative evidence that geography has had a substantial influence on the evolution of ''Banza'' katydids. GenGIS also allows a quantitative analysis of the role of geography to be performed. This is done by drawing a 2D geophylogeny where the leaf nodes are ordered such that they maximize the goodness-of-fit between the tree and geography (Parks and Beiko, 2009; Parks ''et al.'', 2009). To perform this analysis follow these steps:
 # Switch to a top view by clicking on the ''Top view'' toolbar button (Fig. 4).
 # Click on the ''Layout line'' toolbar button (Fig. 10).

@@ Line 65: / Line 65: @@
 =Quantitative Analysis of Geographic Structure=
-The 3D geophylogeny illustrated in Figure 9 provides strong qualitative evidence that geography has had a substantial influence on the evolution of ''Banza'' katydids. GenGIS also allows a quantitative analysis of the role of geography to be performed. This is done by drawing a 2D geophylogeny where the leaf nodes are ordered such that they maximize the goodness-of-fit between the tree and geography [2]. To perform this analysis follow these steps:
+The 3D geophylogeny illustrated in Figure 9 provides strong qualitative evidence that geography has had a substantial influence on the evolution of ''Banza'' katydids. GenGIS also allows a quantitative analysis of the role of geography to be performed. This is done by drawing a 2D geophylogeny where the leaf nodes are ordered such that they maximize the goodness-of-fit between the tree and geography (Parks and Beiko, 2009). To perform this analysis follow these steps:
 # Switch to a top view by clicking on the ''Top view'' toolbar button (Fig. 4).
 # Click on the ''Layout line'' toolbar button (Fig. 10).

@@ Line 3: / Line 3: @@
 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.
-In this tutorial, we consider the phylogenetic tree of Banza katydids (acoustic insects) from the Hawaiian Islands recently recovered by Shapiro ''et al.'', 2006. GenGIS will be used to investigate whether or not this phylogeny is related to the geography of the Hawaiian Islands. A video walkthrough of this tutorial is also available from the GenGIS website [[GenGIS Tutorials]]. To follow along with this tutorial download the data:
+In this tutorial, we consider the phylogenetic tree of Banza katydids (acoustic insects) from the Hawaiian Islands recently recovered by Shapiro ''et al.'', 2006. GenGIS will be used to investigate whether or not this phylogeny is related to the geography of the Hawaiian Islands. A video walkthrough of this tutorial is also available on the [[GenGIS Tutorials | GenGIS website]]. To follow along with this tutorial download the data:
 * [[Media:GenGIS_Katydids_Data.zip|Katydid data set]]

@@ Line 86: / Line 86: @@
 ==Making Movies==
-With minimal effort, fly-through videos can be constructed to help illustrate important aspects of the data. See the GenGIS manual for details on how to modify the camera position through the Python console. A collection of useful functions for creating movies is available in the ''movieHelper.py'' file in the scripts directory. Example movies made with GenGIS can be found on our [[GenGIS|website]].
+With minimal effort, fly-through videos can be constructed to help illustrate important aspects of the data. See the GenGIS manual for details on how to modify the camera position through the Python console. A collection of useful functions for creating movies is available in the ''movieHelper.py'' file in the scripts directory. Example movies made with GenGIS can be found on our [[GenGIS|website]] and details on using the movieHelper.py script is provided in the [[GenGIS Manual]].
 =Contact Information=

@@ Line 55: / Line 55: @@
 ==Tree Properties==
-To modify the visual properties of the tree, right-click on the tree layer in the ''Layer Tree'' and select ''Properties'' from the pop-up menu. This will bring up the ''Tree Properties Dialog Box'' (Fig. 8). The visual properties of labels for the leaf nodes of a tree can be modified in the ''Labels'' tab. Visual properties of the tree are set in the ''Symbology'' tab. We will discuss many of these properties in the next section, but for now change the ''Line thickness'' to 5, the ''Height'' of the tree to 0.3, the tree ''Style'' to ''Propogate discrete colours, and the ''Internal node radius'' to zero as shown in Figure 8. Click ''Apply'' when done and observe how the colours of branches in the tree now correlate with the location colours (Fig. 9). Colours are propagate up from the leaf nodes of the tree until the children of a node have different colours, at which point the default colour will be used for all branches above this node.
+To modify the visual properties of the tree, right-click on the tree layer in the ''Layer Tree'' and select ''Properties'' from the pop-up menu. This will bring up the ''Tree Properties Dialog Box'' (Fig. 8). The visual properties of labels for the leaf nodes of a tree can be modified in the ''Labels'' tab. Visual properties of the tree are set in the ''Symbology'' tab. We will discuss many of these properties in the next section, but for now change the ''Line thickness'' to 5, the ''Relative height'' of the tree to 0.3, the tree ''Style'' to ''Propogate discrete colours, and the ''Internal node radius'' to zero as shown in Figure 8. Click ''Apply'' when done and observe how the colours of branches in the tree now correlate with the location colours (Fig. 9). Colours are propagate up from the leaf nodes of the tree until the children of a node have different colours, at which point the default colour will be used for all branches above this node.
 [[Image:TreeProperties.png|thumb|center|395px|Figure 8. The Tree Properties Dialog Box provides information about a geographic tree model and allows visual properties of the tree to be modified.]]

@@ Line 92: / Line 92: @@
 =References=
-L.H. Shapiro, J.S. Strazanac, and G. K. Roderick. (2006) Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago. ''Mol. Phylogenet. Evol.'' '''41''':53-63. [http://www.ncbi.nlm.nih.gov/pubmed/16781170 Pubmed]
+Shapiro LH, Strazanac JS, and Roderick GK. 2006. Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago. ''Mol. Phylogenet. Evol.'' '''41''':53-63. [http://www.ncbi.nlm.nih.gov/pubmed/16781170 Pubmed]
-D.H. Parks and R.G. Beiko. (2009) Quantitative Visualizations of Hierarchically Organized Data in a Geographic Context. ''27th International Conference on Geoinformatics'', Fairfax, Virgina. [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&isnumber=5292806&arnumber=5293552&count=243&index=6 IEEE Xplore]
+Parks DH and Beiko RG. 2009. Quantitative Visualizations of Hierarchically Organized Data in a Geographic Context. ''27th International Conference on Geoinformatics'', Fairfax, Virgina. [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&isnumber=5292806&arnumber=5293552&count=243&index=6 IEEE Xplore]

← Older revision		Revision as of 13:10, 2 March 2012
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	L.H. Shapiro, J.S. Strazanac, and G. K. Roderick. (2006) Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago. ''Mol. Phylogenet. Evol.'' '''41''':53-63. [http://www.ncbi.nlm.nih.gov/pubmed/16781170 Pubmed]		L.H. Shapiro, J.S. Strazanac, and G. K. Roderick. (2006) Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago. ''Mol. Phylogenet. Evol.'' '''41''':53-63. [http://www.ncbi.nlm.nih.gov/pubmed/16781170 Pubmed]

−	D.H. Parks and R.G. Beiko. (2009) Quantitative Visualizations of Hierarchically Organized Data in a Geographic Context. ''27th International Conference on Geoinformatics'', Fairfax, Virgina.	+	D.H. Parks and R.G. Beiko. (2009) Quantitative Visualizations of Hierarchically Organized Data in a Geographic Context. ''27th International Conference on Geoinformatics'', Fairfax, Virgina. [http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&isnumber=5292806&arnumber=5293552&count=243&index=6 IEEE Xplore]

@@ Line 57: / Line 57: @@
 To modify the visual properties of the tree, right-click on the tree layer in the ''Layer Tree'' and select ''Properties'' from the pop-up menu. This will bring up the ''Tree Properties Dialog Box'' (Fig. 8). The visual properties of labels for the leaf nodes of a tree can be modified in the ''Labels'' tab. Visual properties of the tree are set in the ''Symbology'' tab. We will discuss many of these properties in the next section, but for now change the ''Line thickness'' to 5, the ''Height'' of the tree to 0.3, the tree ''Style'' to ''Propogate discrete colours, and the ''Internal node radius'' to zero as shown in Figure 8. Click ''Apply'' when done and observe how the colours of branches in the tree now correlate with the location colours (Fig. 9). Colours are propagate up from the leaf nodes of the tree until the children of a node have different colours, at which point the default colour will be used for all branches above this node.
-[[Image:MapProperties.png|thumb|center|427px|Figure 8. The Tree Properties Dialog Box provides information about a geographic tree model and allows visual properties of the tree to be modified.]]
+[[Image:TreeProperties.png|thumb|center|395px|Figure 8. The Tree Properties Dialog Box provides information about a geographic tree model and allows visual properties of the tree to be modified.]]
 Your Viewport should now be similar to Figure 9. Assigning colours to locations based on their geographic region emphasizes the role of geography on the evolution of ''Banza'' katydids. As an exercise, try colouring the locations based on Species. This produces a similar tree, but places more emphases on the position of different species in the tree.

@@ Line 45: / Line 45: @@
 ==Map Properties==
 To modify the visual properties of the map, right-click on the map layer in the ''Layer Tree'' and select ''Properties'' from the pop-up menu. This will bring up the ''Map Properties Dialog Box'' (Fig. 6). This dialog box consists of three sections or tabs. On the ''General'' tab, the name of the map can be changed and general information about the layer is provided. The ''Metadata'' tab indicates specific properties of the map such as its dimensions and geographical extents. Visual properties of the map can be set in the ''Symbology'' tab. The ''Colour Map'' sub-tab allows users to specify how colours are mapped to elevation. Modify the properties on this page so they reflect those given in Figure 6 and then hit the ''Apply'' button. This will update the map with the new colour map. Under the ''Advanced'' sub-tab, set the ''Vertical Exaggeration'' to 10 and hit ''Apply''. This scales the elevation of each point in the map which can be useful for visualizing differences in elevation. Click ''OK'' to exit the property dialog.
 ==Location Set Properties==