X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpca.html;h=86097eae50d6c0586d2c146c1608bc8d9a1e0260;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=49019a7ec2541b44b465fb4090c8b1992ef49f04;hpb=2ff5639e0ba863bf19212971977524f0a3c955be;p=jalview.git diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index 49019a7..86097ea 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -1,22 +1,24 @@ + --> Principal Component Analysis @@ -32,12 +34,13 @@ for very large sets of sequences - usually because the JVM has run out of memory. A future release of Jalview will be able to avoid this by executing the calculation via a web service.

-

About PCAPrincipal components analysis is a technique for examining the +

About PCA

+

Principal components analysis is a technique for examining the structure of complex data sets. The components are a set of dimensions -formed from the measured values in the data set, and the principle +formed from the measured values in the data set, and the principal component is the one with the greatest magnitude, or length. The sets of measurements that differ the most should lie at either end of this -principle axis, and the other axes correspond to less extreme patterns +principal axis, and the other axes correspond to less extreme patterns of variation in the data set.

@@ -52,26 +55,26 @@ of variation in the data set.

href="scorematrices.html#simplenucleotide">simple single nucleotide substitution matrix. The options available for calculation are given in the - Change Parameters menu.
Jalview allows - two types of PCA calculation. The default - Jalview PCA Calculation mode (indicated when - that option is ticked in the - Change Parameters menu) of the viewer - performs PCA on a matrix where elements in the upper diagonal give the - sum of scores for mutating in one direction, and the lower diagonal is - the sum of scores for mutating in the other. For protein substitution - models like BLOSUM62, this gives an asymmetric matrix, and a different - PCA to one produced with the method described in the paper by G. - Casari, C. Sander and A. Valencia. Structural Biology volume 2, no. 2, - February 1995 (Change Parameters menu.

+

+ PCA Calculation modes
+ The default Jalview calculation mode + (indicated when Jalview PCA Calculation is + ticked in the Change Parameters menu) is to + perform a PCA on a matrix where elements in the upper diagonal give + the sum of scores for mutating in one direction, and the lower + diagonal is the sum of scores for mutating in the other. For protein + substitution models like BLOSUM62, this gives an asymmetric matrix, + and a different PCA to a matrix produced with the method described in the + paper by G. Casari, C. Sander and A. Valencia. Structural Biology + volume 2, no. 2, February 1995 (pubmed) - and implemented at the SeqSpace server at the EBI. The original method - preconditions the matrix by multiplying it with its transpose, and - this mode is enabled by unchecking the - Jalview PCA Calculation option in the - Change Parameters menu. + and implemented at the SeqSpace server at the EBI. This method + preconditions the matrix by multiplying it with its transpose, and can be employed in the PCA viewer by unchecking the Jalview + PCA Calculation option in the Change + Parameters menu.

- +

The PCA Viewer

This is an interactive display of the sequences positioned within the similarity space, as points in a rotateable 3D scatterplot. The