Description
PCA class generated from dat() function with type="PCA". This object contains the results of the PCA on the data matrix as well as the arguments used.
Usage
"explo.plot"(object, samples = 1:2, plottype = "scores", factor = NULL)
"dat2save"(object)
Arguments
object
Object generated from dat() function.
samples
Principal components to be plotted. If NULL, the two first components are plotted.
plottype
If plottype="scores", the experimental samples are displayed in the plot and colored according to the values of the selected factor.
If plottype="loadings", the genes are plotted.
factor
The samples in the score plot will be colored according to the values of the selected factor. If NULL, the first factor is chosen.
Slots/List Components
An object of this class contains an element (dat) which is a list with the following components: result: List containing the output of PCA. It contains the following elements: "eigen" (eigenvalues and eigenvectors from the PCA decomposition),
"var.exp" (variance explained by each Principal Component), "scores" (coefficients of samples in each PC), "loadings" (coefficients of genes in each PC). factors: Data.frame with factors inherited from object generated by readData() function. norm: Value provided for argument "norm". logtransf: Value provided for argument "logtransf".Methods
This class has an specific show method in order to work and print
a summary of the elements which are contained and a dat2save method
to save the relevant information in an object cleanly. It also has an
explo.plot method to plot the data contained in the object.