SampleIdentificationCenter-class.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/panel_SampleIdentificationCenter.R
\docType{methods}
\name{SampleIdentificationCenter-class}
\alias{SampleIdentificationCenter-class}
\alias{SampleIdentificationCenter}
\alias{.createObservers,SampleIdentificationCenter-method}
\alias{.defineDataInterface,SampleIdentificationCenter-method}
\alias{.defineOutput,SampleIdentificationCenter-method}
\alias{.definePanelTour,SampleIdentificationCenter-method}
\alias{.fullName,SampleIdentificationCenter-method}
\alias{.generateOutput,SampleIdentificationCenter-method}
\alias{.multiSelectionResponsive,SampleIdentificationCenter-method}
\alias{.panelColor,SampleIdentificationCenter-method}
\alias{.renderOutput,SampleIdentificationCenter-method}
\alias{initialize,SampleIdentificationCenter-method}
\title{The SampleIdentificationCenter class}
\value{
A panel designed to work within the iSEE framework
}
\description{
The SampleIdentificationCenter is a \link[iSEE:Panel-class]{iSEE::Panel} subclass that is dedicated
to generating ready-to-use R code for assigning a sample label to samples
received by a selection from another panel.
}
\section{Slot overview}{

The following slots control the behavior of the panel:
\itemize{
\item \code{EditorUsageMode}, a logical scalar determining whether to show
the full R command for making the sample label assignments (if \code{FALSE},
displays the sample id list as plain text).
\item \code{AnnotationRationale}, a string specifying the rationale for the
sample label assignment.
\item \code{CellTypeLabel}, a string providing the label to assign to the
selected samples.
\item \code{ColDataColumn}, a string indicating the name of the colData
column to store the assigned labels.
}

In addition, this class inherits all slots from its parent \link[iSEE:Panel-class]{iSEE::Panel}
class.
}

\section{Constructor}{

\code{SampleIdentificationCenter(...)} creates an instance of a
\code{SampleIdentificationCenter} class,
where any slot and its value can be passed to \code{...} as a named argument.
}

\section{Supported methods}{

In the following code snippets, \code{x} is an instance of a
\link[=SampleIdentificationCenter-class]{SampleIdentificationCenter} class.
}

\examples{
library(iSEE)
library(scRNAseq)

# Example data ----
sce <- ReprocessedAllenData(assays = "tophat_counts")
class(sce)

library(scater)
library(scrapper)
sce <- normalizeRnaCounts.se(sce, assay.type = "tophat_counts", size.factors = NULL)

sce <- runPCA(sce, ncomponents=4)
sce <- runTSNE(sce)
rowData(sce)$ave_count <- rowMeans(assay(sce, "tophat_counts"))
rowData(sce)$n_cells <- rowSums(assay(sce, "tophat_counts") > 0)

# launch the app itself ----

if (interactive()) {
  iSEE(sce, initial = list(
       ReducedDimensionPlot(),
       SampleIdentificationCenter(
         ColumnSelectionSource = "ReducedDimensionPlot1"
      )
    )
  )
}

}
\seealso{
\link[iSEE:Panel-class]{iSEE::Panel}, for the base class.
}
\author{
Federico Marini
}