rliger (version 1.0.1)

makeRiverplot: 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.

Usage

makeRiverplot(
  object,
  cluster1,
  cluster2,
  cluster_consensus = NULL,
  min.frac = 0.05,
  min.cells = 10,
  river.yscale = 1,
  river.lty = 0,
  river.node_margin = 0.1,
  label.cex = 1,
  label.col = "black",
  lab.srt = 0,
  river.usr = NULL,
  node.order = "auto"
)

Value

NULL for now. Could be back if CRAN dependency riverplot is back.

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.

Examples

if (FALSE) {
# Riverplot currently archived, cannot run this example
# ligerex (liger object), factorization complete input
# toy clusters
cluster1 <- sample(c('type1', 'type2', 'type3'), ncol([e-mail][[1]]), replace = TRUE)
names(cluster1) <- colnames([e-mail][[1]])
cluster2 <- sample(c('type4', 'type5', 'type6'), ncol([e-mail][[2]]), replace = TRUE)
names(cluster2) <- colnames([e-mail][[2]])
# create riverplot
makeRiverplot(ligerex, cluster1, cluster2)
}