AMR/man/pca.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pca.R
\name{pca}
\alias{pca}
\title{Principal Component Analysis (for AMR)}
\usage{
pca(
  x,
  ...,
  retx = TRUE,
  center = TRUE,
  scale. = TRUE,
  tol = NULL,
  rank. = NULL
)
}
\arguments{
\item{x}{a \link{data.frame} containing numeric columns}

\item{...}{columns of \code{x} to be selected for PCA}

\item{retx}{a logical value indicating whether the rotated variables
    should be returned.}

\item{center}{a logical value indicating whether the variables
    should be shifted to be zero centered. Alternately, a vector of
    length equal the number of columns of \code{x} can be supplied.
    The value is passed to \code{scale}.}

\item{scale.}{a logical value indicating whether the variables should
    be scaled to have unit variance before the analysis takes
    place.  The default is \code{FALSE} for consistency with S, but
    in general scaling is advisable.  Alternatively, a vector of length
    equal the number of columns of \code{x} can be supplied.  The
    value is passed to \code{\link{scale}}.}

\item{tol}{a value indicating the magnitude below which components
    should be omitted. (Components are omitted if their
    standard deviations are less than or equal to \code{tol} times the
    standard deviation of the first component.)  With the default null
    setting, no components are omitted (unless \code{rank.} is specified
    less than \code{min(dim(x))}.).  Other settings for tol could be
    \code{tol = 0} or \code{tol = sqrt(.Machine$double.eps)}, which
    would omit essentially constant components.}

\item{rank.}{optionally, a number specifying the maximal rank, i.e.,
    maximal number of principal components to be used.  Can be set as
    alternative or in addition to \code{tol}, useful notably when the
    desired rank is considerably smaller than the dimensions of the matrix.}
}
\value{
An object of classes \link{pca} and \link{prcomp}
}
\description{
Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables.
}
\details{
The \code{\link[=pca]{pca()}} function takes a \link{data.frame} as input and performs the actual PCA with the \R function \code{\link[=prcomp]{prcomp()}}.

The result of the \code{\link[=pca]{pca()}} function is a \link{prcomp} object, with an additional attribute \code{non_numeric_cols} which is a vector with the column names of all columns that do not contain numeric values. These are probably the groups and labels, and will be used by \code{\link[=ggplot_pca]{ggplot_pca()}}.
}
\section{Maturing lifecycle}{

\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
}

\examples{
# `example_isolates` is a dataset available in the AMR package.
# See ?example_isolates.

# calculate the resistance per group first
library(dplyr)
resistance_data <- example_isolates \%>\% 
  group_by(order = mo_order(mo),       # group on anything, like order
           genus = mo_genus(mo)) \%>\%   #  and genus as we do here
  summarise_if(is.rsi, resistance)     # then get resistance of all drugs
  
# now conduct PCA for certain antimicrobial agents
pca_result <- resistance_data \%>\%         
  pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT) 
  
pca_result
summary(pca_result)
biplot(pca_result)
ggplot_pca(pca_result) # a new and convenient plot function
}