![[Deprecated]](figures/lifecycle-deprecated.svg)
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.
Arguments
- object
ligerobject. Should run quantileAlignSNF before calling.- cluster1
Cluster assignments for dataset 1. Note that cluster names should be distinct across datasets.
- cluster2
Cluster assignments for dataset 2. Note that cluster names should be distinct across datasets.
- cluster_consensus
Optional external consensus clustering (to use instead of object clusters)
- min.frac
Minimum fraction of cluster for edge to be shown (default 0.05).
- min.cells
Minumum number of cells for edge to be shown (default 10).
- river.yscale
y-scale to pass to riverplot -- scales the edge with values by this factor, can be used to squeeze vertically (default 1).
- river.lty
Line style to pass to riverplot (default 0).
- river.node_margin
Node_margin to pass to riverplot -- how much vertical space to keep between the nodes (default 0.1).
- label.cex
Size of text labels (default 1).
- label.col
Color of text labels (defualt "black").
- lab.srt
Angle of text labels (default 0).
- river.usr
Coordinates at which to draw the plot in form (x0, x1, y0, y1).
- 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
object with refined cluster assignment updated in
"louvain_cluster" variable in cellMeta slot. Can be fetched
with object$louvain_cluster