plot-shc.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/shc-plot.R
\name{plot-shc}
\alias{plot-shc}
\alias{plot.shc}
\title{plot shc object}
\usage{
\method{plot}{shc}(x, groups = NULL, use_labs = TRUE, hang = -1,
  fwer = TRUE, alpha = NULL, ci_idx = NULL, ci_emp = NULL, ...)
}
\arguments{
\item{x}{a \code{shc} object to plot produced by a call to \code{shc}}

\item{groups}{a vector specifying group labels for the clustered objects.
The vector should be in the same order as the rows of the original 
data matrix. If specified, color blocks will be placed along the 
bottom of the dendrogram. Useful when the samples have a priori known
groupi behavior. (default = \code{NULL})}

\item{use_labs}{a boolean specifyin whether rowlabels should be added as 
text along the bottom of the dendrogram (default = \code{TRUE})}

\item{hang}{a double value corresponding to the \code{hang} parameter for 
the typical call to \code{plot} for an object of class
\code{hsigclust} (default = -1)}

\item{fwer}{a boolean specifying whether the FWER control procedure of 
Meinshausen et al. 2010 should be used. (default = \code{TRUE})}

\item{alpha}{a double between 0 and 1 specifying the significance cutoff. If 
\code{fwer} is TRUE, the FWER of the entire dendrogram is controlled at 
\code{alpha}, else, each branch is tested at \code{alpha}. Only has
effect if \code{alpha(shc)} = 1. (default = 0.05 or
\code{alpha} used for \code{x} if original \code{shc} called
with \code{alpha} < 1)}

\item{ci_idx}{a numeric value between 1 and \code{length(ci)} 
specifiying which CI to use for the FWER stopping rule.
This only has an effect if \code{alpha} < 1. (default = 1 or
\code{ci_idx} used for \code{x} if original \code{shc} called with
\code{alpha} < 1 or \code{fwer} = TRUE)}

\item{ci_emp}{a logical value specifying whether to use the empirical
p-value from the CI based on \code{ci_idx} for the FWER stopping rule.
As with \code{ci_idx} this only has an effect if \code{alpha} < 1.
(default = FALSE or \code{ci_emp} used for \code{x} if original \code{shc}
called with \code{alpha} < 1 or \code{fwer} = TRUE)}

\item{...}{other parameters to be used by the function}
}
\value{
\code{ggplot} object containing a dendrogram annotated by the results of the
corresponding \code{shc} analysis
}
\description{
Visualize the results of SHC analysis as an annotated 
dendrogram with significant branches highlighted
}
\details{
This function makes use of dendrogram plotting functions made
available through the \pkg{ggdendro} package which provides a
\pkg{ggplot2}-like grammer for working with dendrograms.
}
\author{
Patrick Kimes
}