Thanks for that Lee.
While I understand that the relationship between the points in the plot is the most important feature, as you explain above, I am still a little confused.
Why are the scales on the axes different, but the actual length of the axes the same on the screen? Doesn’t this essentially squash the plot?
For example, in the following analysis I ordinated the [mean abundance of] aquatic invertebrate communities at four sites over five sampling rounds (i.e. Site 1, Round 2 = 12 etc…).
This is the patn plot. Note the nice-ish division between the dry season samples on the left (numbers ending in 1 or 4), and the wet season samples on the right (numbers ending in 2, 3 or 5).
The x axis covers a range of 1.695, while the y axis covers a range of 2.128. However, the actual axes themselves are the same length.
Exported into sigmaplot, the ordination looks like this (note the even axes). The relationship between the points (which you stress above) has changed because the axes are no longer squashed.
Is this a bug in patn, or am I missing the ‘point’ 😉 (i.e. are the axes actually measuring different things (therefore actually different scales)?
Or, is it because as you state here (http://patn.org/phpBB2/viewtopic.php?t=34), the “result will not have axes that in any way correspond to the SSH axes. SSH simply aims to get the maximum information in the selected number of axes.”
Here is the dataset f.y.i. (the Unidentified variable was made extrinsic, and the columns were log transformed prior to analysis, Bray Curtis w/ default settings).
And the project background:
Tom (user id = rainman)