@@ -11,11 +11,11 @@ ColumnGraphPlot class, where any slot and its value can be passed to

 \code{...} as a named argument.

 }

 \description{

-Hierarchical tree for the rows of a

-\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-constructor]{TreeSummarizedExperiment}}

-object. The tree can be produced with \code{\link[mia:taxonomy-methods]{addTaxonomyTree}}

-and gets stored in the \code{\link[TreeSummarizedExperiment:rowLinks]{rowTree}}

-slot of the experiment object. The panel implements \code{\link[miaViz:plotTree]{plotRowTree}}

+Network organisation for the samples of a

+\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}

+object. The igraph should be stored in the \code{metadata} slot by a name

+containing \code{"graph"}. This panel uses

+\code{\link[miaViz:plotColGraph]{plotColGraph}}

 to generate the plot.

 }

 \section{Slot overview}{

@@ -25,10 +25,17 @@ This class inherits all slots from its parent class \linkS4class{GraphPlot}.

 }

 \examples{

-# Import TreeSE

 library(mia)

-data("Tengeler2020", package = "mia")

-tse <- Tengeler2020

+library(miaViz)

+data("GlobalPatterns", library = "mia")

+data("col_graph", library = "miaViz")

+

+tse <- GlobalPatterns

+tse <- agglomerateByRank(tse,

+                         rank = "Genus",

+                         na.rm = TRUE)

+                         

+metadata(tse)$graph <- col_graph

 # Store panel into object

 panel <- ColumnGraphPlot()

@@ -40,6 +47,10 @@ if (interactive()) {

   iSEE(tse, initial = c(panel))

 }

+}

+\seealso{

+\linkS4class{GraphPlot}

+\linkS4class{RowGraphPlot}

 }

 \author{

 Giulio Benedetti

new file mode 100644

@@ -0,0 +1,46 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/AllClasses.R, R/class-ColumnGraphPlot.R

+\docType{class}

+\name{ColumnGraphPlot-class}

+\alias{ColumnGraphPlot-class}

+\alias{ColumnGraphPlot}

+\title{Column graph plot}

+\value{

+The \code{ColumnGraphPlot(...)} constructor creates an instance of a

+ColumnGraphPlot class, where any slot and its value can be passed to

+\code{...} as a named argument.

+}

+\description{

+Hierarchical tree for the rows of a

+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-constructor]{TreeSummarizedExperiment}}

+object. The tree can be produced with \code{\link[mia:taxonomy-methods]{addTaxonomyTree}}

+and gets stored in the \code{\link[TreeSummarizedExperiment:rowLinks]{rowTree}}

+slot of the experiment object. The panel implements \code{\link[miaViz:plotTree]{plotRowTree}}

+to generate the plot.

+}

+\section{Slot overview}{

+

+

+This class inherits all slots from its parent class \linkS4class{GraphPlot}.

+}

+

+\examples{

+# Import TreeSE

+library(mia)

+data("Tengeler2020", package = "mia")

+tse <- Tengeler2020

+

+# Store panel into object

+panel <- ColumnGraphPlot()

+# View some adjustable parameters

+head(slotNames(panel))

+

+# Launch iSEE with custom initial panel

+if (interactive()) {

+  iSEE(tse, initial = c(panel))

+}

+

+}

+\author{

+Giulio Benedetti

+}