% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/visualization.R
\name{makeRiverplot-deprecated}
\alias{makeRiverplot-deprecated}
\title{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Generate a river (Sankey) plot}
\arguments{
\item{object}{\code{liger} object. Should run quantileAlignSNF before calling.}

\item{cluster1}{Cluster assignments for dataset 1. Note that cluster names
should be distinct across datasets.}

\item{cluster2}{Cluster assignments for dataset 2. Note that cluster names
should be distinct across datasets.}

\item{cluster_consensus}{Optional external consensus clustering (to use
instead of object clusters)}

\item{min.frac}{Minimum fraction of cluster for edge to be shown (default
0.05).}

\item{min.cells}{Minumum number of cells for edge to be shown (default 10).}

\item{river.yscale}{y-scale to pass to riverplot -- scales the edge with
values by this factor, can be used to squeeze vertically (default 1).}

\item{river.lty}{Line style to pass to riverplot (default 0).}

\item{river.node_margin}{Node_margin to pass to riverplot -- how much
vertical space to keep between the nodes (default 0.1).}

\item{label.cex}{Size of text labels (default 1).}

\item{label.col}{Color of text labels (defualt "black").}

\item{lab.srt}{Angle of text labels (default 0).}

\item{river.usr}{Coordinates at which to draw the plot in form (x0, x1, y0,
y1).}

\item{node.order}{Order of clusters in each set (list with three vectors of
ordinal numbers). By default will try to automatically order them
appropriately.}
}
\value{
\code{object} with refined cluster assignment updated in
\code{"louvain_cluster"} variable in \code{cellMeta} slot. Can be fetched
with \code{object$louvain_cluster}
}
\description{
Creates a riverplot to show how separate cluster assignments from two
datasets map onto a joint clustering. The joint clustering is by default the
object clustering, but an external one can also be passed in. Uses the
riverplot package to construct riverplot object and then plot.
}
\seealso{
\code{\link{rliger-deprecated}}
}
