X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpca.html;h=f7afef43dad88b3e9f16ad3bad009fc1bd6fe8b9;hb=e66bdc1c0086ab56c56979d9dc6635e81503eb84;hp=5f67fc250814c5f51f6b8eeadb4f4fdaa5313201;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index 5f67fc2..f7afef4 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -1,6 +1,109 @@ - - -
-pca
- - + + + +Principal Component Analysis
+This calculation creates a spatial representation of the +similarities within a selected group, or all of the sequences in an +alignment. After the calculation finishes, a 3D viewer displays the set +of sequences as points in 'similarity space', and similar sequences tend +to lie near each other in the space.
+Caveats
The calculation is computationally expensive, and may fail
+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 +structure of complex data sets. The components are a set of dimensions +formed from the measured values in the data set, and the principle +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 +of variation in the data set.
+ +
+ Calculating PCAs for aligned sequences
Jalview can
+ perform PCA analysis on both proteins and nucleotide sequence
+ alignments. In both cases, components are generated by an eigenvector
+ decomposition of the matrix formed from the sum of substitution matrix
+ scores at each aligned position between each pair of sequences -
+ computed either with BLOSUM62 or the 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 (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.
+
The PCA Viewer
+This is an interactive display of the sequences positioned within +the similarity space, as points in a rotateable 3D scatterplot. The +colour of each sequence point is the same as the sequence group colours, +white if no colour has been defined for the sequence, and green if the +sequence is part of a the currently selected group.
+The 3d view can be rotated by dragging the mouse with the left +mouse button pressed. The view can also be zoomed in and out with the up +and down arrow keys (and the roll bar of the mouse if +present). Labels will be shown for each sequence if the entry in the +View menu is checked, and the plot background colour changed from the +View→Background Colour.. dialog box. The File menu allows the view +to be saved (File→Save submenu) as an EPS or PNG +image or printed, and the original alignment data and matrix resulting +from its PCA analysis to be retrieved. The coordinates for the whole PCA +space, or just the current view may also be exported as CSV files for +visualization in another program or further analysis.
+
Options for coordinates export are:
+A tool tip gives the sequence ID corresponding to a point in the +space, and clicking a point toggles the selection of the corresponding +sequence in the associated alignment window views. By default, +points are only associated with the alignment view from which the PCA +was calculated, but this may be changed via the View→Associate +Nodes sub-menu.
+Initially, the display shows the first three components of the +similarity space, but any eigenvector can be used by changing the +selected dimension for the x, y, or z axis through each ones menu +located below the 3d display. The Reset button will reset axis and rotation settings to their defaults.
++
+The output of points and transformed point coordinates was added to the Jalview desktop in v2.7. +The Reset button and Change Parameters menu were added in Jalview 2.8. + +