GOS Tutorial - Revision history

Beiko at 16:49, 13 March 2012

2012-03-13T16:49:31Z

Dparks: /* Loading Data */

2012-03-02T20:33:05Z

Loading Data

Dparks: /* Quantitative Analysis of Geographic Structure */

2012-03-02T19:13:15Z

Quantitative Analysis of Geographic Structure

Dparks: /* Introduction */

2012-03-02T19:11:58Z

Introduction

Dparks: /* Introduction */

2012-03-02T19:11:26Z

Introduction

Dparks at 18:41, 2 March 2012

2012-03-02T18:41:43Z

Dparks: /* Making Movies */

2012-03-02T18:41:25Z

Making Movies

Dparks: /* Making Movies */

2012-03-02T18:41:10Z

Making Movies

Dparks: /* Quantitative Analysis of Geographic Structure */

2012-03-02T18:40:43Z

Quantitative Analysis of Geographic Structure

Dparks: /* Quantitative Analysis of Geographic Structure */

2012-03-02T18:39:39Z

Quantitative Analysis of Geographic Structure

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 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 examine samples collected as part of the Global Ocean Sampling expedition (Rusch et al., 2007) in order to investigate the influence of environmental factors on the composition of microbial communities from marine ecosystems. A more thorough analysis of this data is available in Parks ''et al.'', 2009. This tutorial demonstrates how to load data, illustrates how to change visual properties, presents a detail analysis of the geographic structure of these microbial communities, and examines the distribution of taxa within these samples. A video walkthrough of this tutorial is also available on the [[GenGIS Tutorials | GenGIS website]]. To follow along with this tutorial download the data:
+In this tutorial, we examine samples collected as part of the Global Ocean Sampling expedition (Rusch et al., 2007) in order to investigate the influence of environmental factors on the composition of microbial communities from marine ecosystems. A more thorough analysis of this data is available in Parks ''et al.'', 2009. This tutorial demonstrates how to load data, illustrates how to change visual properties, presents a detailed analysis of the geographic structure of these microbial communities, and examines the distribution of taxa within these samples. 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_GOS_Data.zip|GOS data set]]

@@ Line 9: / Line 9: @@
 =Loading Data=
-The GOS data  consists of a 2D map (GOS_GS002_GS020.tif), projection information for the map (GOS_GS002_GS020.tfw), location data (atlantic-seaboard-sample-sites.csv), sequence data (atlantic-seaboard-sequence-data.csv), and a UniFrac tree indicating the relative similarity of the microbial communities (asb_unifrac_community_tree.gtm). Load this data into GenGIS. For basic information of using the GenGIS interface and loading data please see the [[Katydid Tutorial | ''Banza'' Katydid Tutorial]].
+The GOS data  consists of a 2D map (GOS_GS002_GS020.tif), projection information for the map (GOS_GS002_GS020.tfw), location data (atlantic-seaboard-sample-sites.csv), sequence data (atlantic-seaboard-sequence-data.csv), and a UniFrac tree indicating the relative similarity of the microbial communities (asb_unifrac_community_tree.gtm). Load this data into GenGIS. For basic information on using the GenGIS interface and loading data please see the [[Katydid Tutorial | ''Banza'' Katydid Tutorial]].
 =Changing Visual Properties=

@@ Line 27: / Line 27: @@
 =Quantitative Analysis of Geographic Structure=
-The 3D geophylogeny suggests that habitat type has a large influence of the relative similarity of these microbial communities. The [[Media:GenGIS_GOS_Tutorial.swf|video tutorial]], [[Katydid Tutorial | ''Banza'' Katydid tutorial]], and the Parks ''et al.'', 2009 manuscript describe how 2D geophylogenies produced by GenGIS can be used to explore the influence of geography on the structure of hierarchically organized data. The remainder of this section assumes you are familiar with the basics of how these analyses are conducted in GenGIS.
+The 3D geophylogeny suggests that habitat type has a large influence of the relative similarity of these microbial communities. The [[Media:GenGIS_GOS_Tutorial.mp4|video tutorial]], [[Katydid Tutorial | ''Banza'' Katydid tutorial]], and the Parks ''et al.'', 2009 manuscript describe how 2D geophylogenies can be analyzed within GenGIS. The remainder of this section assumes you are familiar with the basics of how these analyses are conducted.
 GenGIS allows the number of crossing which occur for ''all'' linear gradients to be explored. Right-click on the subtree of the geophylogeny you wish to analyze and select ''Perform linear axis analysis on subtree''. This will produce a graph showing the number of crossings which occur for all possible linear gradients (Fig. 3). Clicking on the graph causes the linear layout line to rotate to a given orientation. Running a permutation test causes a red line to be drawn on the plot which indicates the number of crossings at which the specified critical value (''i.e.'', ''p''-value = 0.05) is obtained. That is, linear gradients with orientations resulting in fewer crossings are significant at the selected ''p''-value.

@@ 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 examine samples collected as part of the Global Ocean Sampling expedition (Rusch et al., 2007) in order to investigate the influence of environmental factors on the composition of microbial communities from marine ecosystems. A more thorough analysis of this data is available in Parks ''et al.'', 2009. This tutorial demonstrates how to load data, illustrates how to change visual properties, presents a detail analysis of the geographic structure of these microbial communities, and examines the distribution of taxa within these samples. A video walkthrough of this tutorial is also available from the [[GenGIS website]]. To follow along with this tutorial download the data:
+In this tutorial, we examine samples collected as part of the Global Ocean Sampling expedition (Rusch et al., 2007) in order to investigate the influence of environmental factors on the composition of microbial communities from marine ecosystems. A more thorough analysis of this data is available in Parks ''et al.'', 2009. This tutorial demonstrates how to load data, illustrates how to change visual properties, presents a detail analysis of the geographic structure of these microbial communities, and examines the distribution of taxa within these samples. 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_GOS_Data.zip|GOS data set]]

@@ 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 examine samples collected as part of the Global Ocean Sampling expedition (Rusch et al., 2007) in order to investigate the influence of environmental factors on the composition of microbial communities from marine ecosystems. A more thorough analysis of this data is available in Parks ''et al.'', 2009. This tutorial demonstrates how to load data, illustrates how to change visual properties, presents a detail analysis of the geographic structure of these microbial communities, and examines the distribution of taxa within these samples. 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 examine samples collected as part of the Global Ocean Sampling expedition (Rusch et al., 2007) in order to investigate the influence of environmental factors on the composition of microbial communities from marine ecosystems. A more thorough analysis of this data is available in Parks ''et al.'', 2009. This tutorial demonstrates how to load data, illustrates how to change visual properties, presents a detail analysis of the geographic structure of these microbial communities, and examines the distribution of taxa within these samples. A video walkthrough of this tutorial is also available from the [[GenGIS website]]. To follow along with this tutorial download the data:
 * [[Media:GenGIS_GOS_Data.zip|GOS data set]]

@@ Line 10: / Line 10: @@
 The GOS data  consists of a 2D map (GOS_GS002_GS020.tif), projection information for the map (GOS_GS002_GS020.tfw), location data (atlantic-seaboard-sample-sites.csv), sequence data (atlantic-seaboard-sequence-data.csv), and a UniFrac tree indicating the relative similarity of the microbial communities (asb_unifrac_community_tree.gtm). Load this data into GenGIS. For basic information of using the GenGIS interface and loading data please see the [[Katydid Tutorial | ''Banza'' Katydid Tutorial]].
 =Changing Visual Properties=
@@ Line 42: / Line 41: @@
 [[Image:GOS_Pie_Charts.png|thumb|center|600px|Figure 5. Pie charts showing the distribution of key taxa within microbial communities sampled off the Atlantic seaboard.]]
 =Contact Information=

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 [[Image:GOS_Pie_Charts.png|thumb|center|600px|Figure 5. Pie charts showing the distribution of key taxa within microbial communities sampled off the Atlantic seaboard.]]
-==Making Movies==
+=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]] and details on using the movieHelper.py script is provided in the [[GenGIS Manual]].

@@ Line 28: / Line 28: @@
 =Quantitative Analysis of Geographic Structure=
-The 3D geophylogeny suggests that habitat type has a large influence of the relative similarity of these microbial communities. The [[Media:GenGIS_GOS_Tutorial.swf|video tutorial]], [[Katydid Tutorial | ''Banza'' Katydid tutorial]], and the Parks ''et al.'', 2009 manuscript describe how 2D geophylogenies produced by GenGIS can be used to explore the influence of geography on the structure of hierarchically organized data. The remainder of this section assumes you are familiar with the basics of how 2D geophylogenies are analyzed in GenGIS.
+The 3D geophylogeny suggests that habitat type has a large influence of the relative similarity of these microbial communities. The [[Media:GenGIS_GOS_Tutorial.swf|video tutorial]], [[Katydid Tutorial | ''Banza'' Katydid tutorial]], and the Parks ''et al.'', 2009 manuscript describe how 2D geophylogenies produced by GenGIS can be used to explore the influence of geography on the structure of hierarchically organized data. The remainder of this section assumes you are familiar with the basics of how these analyses are conducted in GenGIS.
-GenGIS allows the number of crossing which occur for ''all'' linear gradients to be explored. Right-click on the subtree on the geophylogeny you wish to analyze and select ''Perform linear axis analysis on subtree''. This will produce a graph showing the number of crossings which occur for all possible linear gradients (Fig. 3). Clicking on the graph causes the linear layout line to rotate to a given orientation. Running a permutation test causes a red line to be drawn on the plot which indicates the number of crossings at which the specified critical value (''i.e.'', ''p''-value = 0.05) is obtained. That is, linear gradients with orientations resulting in fewer crossings are significant at the selected ''p''-value.
+GenGIS allows the number of crossing which occur for ''all'' linear gradients to be explored. Right-click on the subtree of the geophylogeny you wish to analyze and select ''Perform linear axis analysis on subtree''. This will produce a graph showing the number of crossings which occur for all possible linear gradients (Fig. 3). Clicking on the graph causes the linear layout line to rotate to a given orientation. Running a permutation test causes a red line to be drawn on the plot which indicates the number of crossings at which the specified critical value (''i.e.'', ''p''-value = 0.05) is obtained. That is, linear gradients with orientations resulting in fewer crossings are significant at the selected ''p''-value.
 [[Image:GOS_Linear_Axes_Plot.png|thumb|center|600px|Figure 3. Graph showing the number of crossings for all possible linear gradients.]]