Visualization
of heatmaps:
- The method of visualization is simple; a distance matrix consists
of a two dimensional table that contains pairwise evolutionary distances
among a set of N taxa. The minimum and maximum
values are then determined and numerical values are transformed into a number
of discrete sub-ranges to which color/hue combinations are assigned. At
present, we employ 11 sub-ranges and three colors: green, black, and red.
The more intense the shade of green, the more closely relate are the pair
of sequence. Likewise, the more intense the shade of red, the more distant
the evolutionary distance. Black regions within the matrix represent the
median for the subset of sequences.
- Practical limits are set by hardware capacity. For example, screen
resolution limits the number of samples that can be displayed because,
at best, one distance value can be represented by one pixel. Internet
bandwidth is also a limiting factor.
- To view interactive
heatmaps (which are accessible from the taxonomic atlas and analytics
pages), simply place the cursor over the area of interest. A legend
for the pair of points, or a larger region (in the analytics) will
appear in the upper right hand corner of the plotting region. S-Plus
graphlets support zooming and allow visualization of regions of interest
in greater detail as well.
Visualization of PCA plots:
- Dynamic PCA plots highlight specific taxa in color, against a background
of all taxa (global PCA plots) or subsets of taxa (phyla or class)
based on predefined taxonomic criteria. Placing the cursor over point(s)
of
interest will
provide information about the identity of the point (current name,
RDP-id, higher taxon). For the purpose of comparison, we have included
plots derived from two separate data sets. The unresolved plots contain
a number of unresolved taxonomic and annotation errors, and many previously
unresolved synonymies. The resolved plots were derived from a subset
of those sequences in which the taxonomic and annotation errors were
corrected and the synonymies were resolved to coincide with the taxon
to which the source organism most likely belongs based on 16S rDNA
sequence similarity.
Page
1|2|3|4|5 |
|
