makeRiverplot-deprecated: *[Deprecated]* Generate a river (Sankey) plot

In rliger: Linked Inference of Genomic Experimental Relationships

Generate a river (Sankey) plot

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.

Arguments

object	liger object. 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

See Also

rliger-deprecated

rliger documentation built on Oct. 30, 2024, 1:07 a.m.