Thursday, August 23, 2012

Tracking Attributes in a MDS map.

When using MDS (multidimensional scaling) maps in the practice, a frequently asked question is how does a particular attribute, i.e. a data column in the input table, impact the resulting MDS map? One simple way to visualize the effect of an attribute is just create another MDS map without that attribute under investigation. The  difference between the two maps can be then ascribed to that attribute. For instance, the following two maps are MDS maps (created with CCA aglrotihm) of the VisuMap sample dataset yeast.xvm: the fisrt is created with the first 5 attributes; second one with just the first 4 attributes.

The difference between the two maps above is thus caused by leaving out the fifth attribute (i.e. the attribute spo2). We notice that the two major data point clusters (colored as yellow and cyan)  are more separated in the first map. Thus, we can see that the attribute spo2 provides significant separation for these two clusters.

With the VisuMap plugin module ClipRecorder we can do a much better job to visualize the effect of a attribute. The newly released ClipRecorder version 1.2 includes scripts that help users to create a sequence of MDS maps with gradually decreasing weight for a selected attributes.  The difference between two successive maps provides direction vectors which indicate how data points move when the weight for the selected attributes decreases. The following map is one of such map that visualizes the movement direction of all data points at certain moment during the running process of the script:

In above map, each bi-colored bar represents a data point; the red side of the bar points to the moving direction of a data point and the length of the bar indicates the speed of the movement.

The ClipRecorder plugin also records all the map sequences, so that we can replay them any time later as simple map animation. The following short video clip, for instance, shows such an animation:

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