`pca()`

Computes a Principal Component Analysis. It wrappers`stats::prcomp()`

, but returns more results such as data, scores, contributions and quality of measurements for individuals and variables.`get_biplot()`

: Produces a biplot for an object computed with`pca()`

.`plot.pca()`

: Produces several types of plots, depending on the`type`

and`which`

arguments.`type = "var"`

Produces a barplot with the contribution (`which = "contrib"`

), qualitity of adjustment`which = "cos2"`

, and a scatter plot with coordinates (`which = "coord"`

) for the variables.`type = "ind"`

Produces a barplot with the contribution (`which = "contrib"`

), qualitity of adjustment`which = "cos2"`

, and a scatter plot with coordinates (`which = "coord"`

) for the individuals.`type = "biplot"`

Produces a biplot.

## Arguments

- x
For

`pca()`

, a numeric or complex matrix (or data frame) which provides the data for the principal components analysis.For

`plot.pca()`

and`get_biplot()`

, an object computed with`pca()`

.

- scale
A logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place. Defaults to

`TRUE`

.- axes
The principal component axes to plot. Defaults to

`axes = c(1, 2)`

, i.e., the first and second interaction principal component axis.- show
Which to show in the biplot. Defaults to

`"both"`

(both variables and individuals). One can also use`"var"`

, or`"ind"`

.- show_ind_id
Shows the labels for individuals? Defaults to

`TRUE`

.- show_unit_circle
Shows the unit variance circle? Defaults to

`TRUE`

.- expand
An expansion factor to apply when plotting the second set of points relative to the first. This can be used to tweak the scaling of the two sets to a physically comparable scale. Setting to

`TRUE`

will automatically compute the expansion factor. Alternatively, a numeric value can be informed.- type
One of

`"var"`

(to plot variables),`"ind"`

(to plot individuals), or`"biplot"`

to create a biplot.- which
Which measure to plot. Either

`which = "contribution"`

(default),`which = "cos2"`

(quality of representation), or`which = "coord"`

(coordinates)- axis
The axist to plot the contribution/cos2. Defaults to 1.

- ...
Further arguments passed on to

`get_biplot()`

when`type = "biplot"`

. Otherwise, When`which = "coord"`

, further arguments passed on to`get_biplot()`

. When`which = "contrib"`

, or`which = "cos2"`

further arguments passed on to`graphics::barplot()`

.

## Value

`pca()`

returns a list including:`data`

: The raw data used to compute the PCA.`variances`

: Variances (eigenvalues), and proportion of explained variance for each component.`center,scale`

: the centering and scaling used.`ind,var`

A list with the following objects for individuals/variables, respectively.`coord`

: coordinates for the individuals/variables (loadings * the component standard deviations)`cos2`

: cos2 for the individuals/variables (coord^2)`contrib`

: The contribution (in percentage) of a variable to a given principal component: (cos2 * 100) / (total cos2 of the component)

`plot.pca()`

returns a list with the coordinates used.`get_biplot()`

returns a`NULL`

object