% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-12th May 2016
+9th June 2016
\end{center}
\subsubsection{What is 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 component is the one with 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
+should lie at either end of this principal axis, and the other axes correspond
to less extreme patterns of variation in the data set.
In this case, the components are generated by an eigenvector decomposition of
the matrix formed from the sum of pairwise substitution scores at each aligned
\subsubsection{The PCA Viewer}
-PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principle
+PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principlal
Component Analysis} menu option. {\bf PCA requires a selection containing at
least 4 sequences}. A window opens containing the PCA tool (Figure \ref{PCA}).
Each sequence is represented by a small square, coloured by the background
representation of the PCA plot can be exported as an EPS or PNG image {\sl via}
the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
-\exercise{Principle Component Analysis}{ \exstep{Load the alignment at
+\exercise{Principal Component Analysis}{ \exstep{Load the alignment at
\textsf{http://www.jalview.org/examples/exampleFile.jar} and press [ESC] to clear any selections. Alternatively, select {\sl Select $\Rightarrow$ Undefine Groups} to remove all groups and colourschemes. } \exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}. A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible. Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window. Note that clicking on points in the plot will highlight them on the alignment and tree. }
\exstep{ Click on the tree window. Careful selection of the tree partition
location will divide the alignment into a number of groups, each of a different
git://source.jalview.org / jalview-manual.git / commitdiff