Cartogram and GCPD Tutorial - Revision history

Beiko: Beiko moved page Aneides lugubris Tutorial to Cartogram and GCPD Tutorial

2017-05-19T20:44:02Z

2017-05-19T20:42:37Z

Phylogenetic transformations using the GCPD

2017-05-19T20:40:59Z

2017-05-19T20:37:24Z

Phylogenetic transformations using the GCPD

2017-05-19T20:17:17Z

Phylogenetic transformations using the GCPD

2017-05-16T16:05:38Z

2017-05-16T16:04:56Z

Location density

2017-05-16T16:03:33Z

Loading Data and Changing Visual Properties

2017-05-16T16:02:59Z

Loading Data and Changing Visual Properties

2017-05-16T16:02:27Z

Loading Data and Changing Visual Properties

@@ Line 74: / Line 74: @@
 [[Image:GCPDSlide3.PNG|center|600px]]
-[[Image:Aneides l15 m5.png|thumb|center|600px|Figure 1. A cartogram created using ''Aneides lugubris'' and a Location Radius value of 15 and a Variable Multiplier of 5.]]
+The arrow shows an area of high phylogenetic diversity - three different clades in one small region of the map - that has been disproportionately been expanded because of the GCPD.
 =Contact Information=

@@ Line 62: / Line 62: @@
 To compute the GCPD, go to the Plugins menu and select the GCPD option.
-***GCPD window option
+[[Image:GCPDSlide1.PNG|center|600px]]
 In this window, you can choose the method for aggregating diversity across pairs of sites, the location and tree layer (which are fixed in our case, since they have only one of each), and the choice whether to use phylogenetic diversity (PD) or 1 - PD to define the distance. Choosing PD will tend to assign large values to sites whose neighbours are phylogenetically distinct, whereas 1 - PD will do the opposite.
@@ Line 68: / Line 68: @@
 Click "Calculate" to compute the GCPD for each point. Once the values have been calculated, select "Add to GenGIS" to add them as an additional location attribute. You can use the Location table viewer plugin to verify that it has been added:
-***Loc table image
+[[Image:GCPDSlide2.PNG|center|600px]]
 Now we're ready to generate the cartogram as before. This time, select "PhylogeneticDistance" from the cartogram menu, and hit "Go!". The following example was generated with a location radius of 5 and a variable multiplier of 30:
-*** GCPDcarto image
+[[Image:GCPDSlide3.PNG|center|600px]]
 [[Image:Aneides l15 m5.png|thumb|center|600px|Figure 1. A cartogram created using ''Aneides lugubris'' and a Location Radius value of 15 and a Variable Multiplier of 5.]]

@@ Line 70: / Line 70: @@
 ***Loc table image
-Now we're ready to generate the cartogram as before. This time, select "PhylogeneticDistance" from the cartogram menu, and hit "Go!"
+Now we're ready to generate the cartogram as before. This time, select "PhylogeneticDistance" from the cartogram menu, and hit "Go!". The following example was generated with a location radius of 5 and a variable multiplier of 30:
 [[Image:Aneides l15 m5.png|thumb|center|600px|Figure 1. A cartogram created using ''Aneides lugubris'' and a Location Radius value of 15 and a Variable Multiplier of 5.]]

@@ Line 58: / Line 58: @@
 ==Phylogenetic transformations using the GCPD==
-GenGIS can use data besides location count to adjust the map. We have developed the Geographically Coupled Phylogenetic Distance to adjust the distortion effects based on phylogenetic diversity.
+GenGIS can use data besides location count to adjust the map. Any quantitative value in the location file can be used for this purpose, but we have developed the Geographically Coupled Phylogenetic Distance (GCPD) to adjust the distortion effects based on phylogenetic diversity. Briefly, the GCPD for a location is computed by considering its diversity relative to the closest other locations in the map.
 [[Image:Aneides l15 m5.png|thumb|center|600px|Figure 1. A cartogram created using ''Aneides lugubris'' and a Location Radius value of 15 and a Variable Multiplier of 5.]]

@@ Line 30: / Line 30: @@
 You should end up with an image that looks like this:
-[[Image:Slide3.PNG|thumb|center|600px]]
+[[Image:Slide3.PNG|center|600px]]
 =Creating Cartograms=
@@ Line 48: / Line 48: @@
 If we hide the tree, then the cartogram should look like this:
-[[Image:Slide5.PNG|thumb|center|600px]]
+[[Image:Slide5.PNG|center|600px]]
 To fine tune the cartogram two parameters can be adjusted: ''Location Radius'' and ''Variable Multiplier''. The ''Location Radius'' adjusts the size of the grid cells the map is divided into when the cartogram is created, while the ''Variable Multiplier'' amplifies the value of populated grid cells by a X times multiple of the stored value.
@@ Line 54: / Line 54: @@
 You can click "Restore Map" in the cartogram tab to reset the map to its original state. Now try setting the location radius to 100 and re-running.
-[[Image:Slide7.PNG|thumb|center|600px]]
+[[Image:Slide7.PNG|center|600px]]
 ==Phylogenetic transformations using the GCPD==

← Older revision	Revision as of 20:44, 19 May 2017
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 Let's go with 10 and 10 for location radius and variable multiplier now. Let's also choose "Resize Density Map" at 50% to increase the speed of the procedure. The percentage controls the decrease when the map is resized, with 60% as the maximum value (in practice, values over 60% give cartograms that are unusable). In general, the larger the values of location radius and variable multiplier, the more pronounced the effect of resizing will be, and the points will track the map less well.
 Click "Go!" to create the cartogram. Note that "Apply" has no effect in this menu.
@@ Line 46: / Line 48: @@
 If we hide the tree, then the cartogram should look like this:
-Cartogram go here...
+[[Image:Slide5.PNG|thumb|center|600px]]
 To fine tune the cartogram two parameters can be adjusted: ''Location Radius'' and ''Variable Multiplier''. The ''Location Radius'' adjusts the size of the grid cells the map is divided into when the cartogram is created, while the ''Variable Multiplier'' amplifies the value of populated grid cells by a X times multiple of the stored value.
@@ Line 52: / Line 54: @@
 You can click "Restore Map" in the cartogram tab to reset the map to its original state. Now try setting the location radius to 100 and re-running.
-Cartogram go here...
+[[Image:Slide7.PNG|thumb|center|600px]]
 ==Phylogenetic transformations using the GCPD==

@@ Line 17: / Line 17: @@
 (2) Change the map colours according to the following scheme:
-[[Image:Slide1.PNG|center|600px]]
+[[Image:Slide1.PNG|600px]]
 (3) Change the vertical exaggeration to 5.
@@ Line 23: / Line 23: @@
 (4) Load the location file, and edit the colours as follows:
-[[Image:Slide2.PNG|center|600px]]
+[[Image:Slide2.PNG|600px]]
 This is the "Continuous: Scientific" colour scale, with the Northern clade set to yellow to increase the contrast.
@@ Line 30: / Line 30: @@
 You should end up with an image that looks like this:
 [[Image:Slide3.PNG|thumb|center|600px]]