% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plotLong.R
\name{plotLong}
\alias{plotLong}
\title{Plot Longitudinal Profiles by Cluster}
\usage{
plotLong(
  object,
  time = NULL,
  plot = TRUE,
  center = TRUE,
  scale = TRUE,
  title = "Time-course Expression",
  X.label = NULL,
  Y.label = NULL,
  legend = FALSE,
  legend.title = NULL,
  legend.block.name = NULL
)
}
\arguments{
\item{object}{a mixOmics result of class (s)pca, (s)pls, block.(s)pls.}

\item{time}{(optional) a numeric vector, the same size as \code{ncol(X)}, to change the time scale.}

\item{plot}{a logical, if TRUE then  a plot is produced. Otherwise, the data.frame on which the plot is based on is returned.}

\item{center}{a logical value indicating whether the variables should be shifted to be zero centered.}

\item{scale}{a logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place.}

\item{title}{character indicating the title plot.}

\item{X.label}{x axis titles.}

\item{Y.label}{y axis titles.}

\item{legend}{a logical, to display or not the legend.}

\item{legend.title}{if \code{legend} is provided, title of the legend.}

\item{legend.block.name}{a character vector corresponding to the size of the number of blocks in the mixOmics object.}
}
\value{
a data.frame (gathered form) containing the following columns:
\item{time}{x axis values}
\item{molecule}{names of features}
\item{value}{y axis values}
\item{cluster}{assigned clusters}
\item{block}{name of 'blocks'}
}
\description{
This function provides a expression profile representation over time and by cluster.
}
\examples{
demo <- suppressWarnings(get_demo_cluster())
X <- demo$X
Y <- demo$Y
Z <- demo$Z

# (s)pca
pca.res <- mixOmics::pca(X, ncomp = 3)
plotLong(pca.res)
spca.res <- mixOmics::spca(X, ncomp =2, keepX = c(15, 10))
plotLong(spca.res)

# (s)pls
pls.res <- mixOmics::pls(X,Y)
plotLong(pls.res)
spls.res <- mixOmics::spls(X,Y, keepX = c(15,10), keepY=c(5,6))
plotLong(spls.res)

# (s)block.spls
block.pls.res <- mixOmics::block.pls(X=list(X=X,Z=Z), Y=Y)
plotLong(block.pls.res)
block.spls.res <- mixOmics::block.spls(X=list(X=X,Z=Z), Y=Y, 
                             keepX = list(X = c(15,10), Z = c(5,6)), 
                             keepY = c(3,6))
plotLong(block.spls.res)


}
\seealso{
\code{\link[timeOmics]{getCluster}}
}