Plots slingshot results

Plots the results of the slingshot analysis using ggplots2

# S3 method for slingshot
plot(
  result,
  clusters = NULL,
  lineages = FALSE,
  pt_size = 0.1,
  line_size = 0.1,
  relevant = FALSE,
  Pseudotime = FALSE,
  Expression = FALSE,
  object = NULL,
  assay = NULL,
  slot = "norm.scaled",
  feature = NULL,
  ...
)

Arguments

result

A SlingshotDataSet class results object

clusters

Vector. A vector of clusters to use in ggplot, if NULL the clusters used to generate results will be used. Default = NULL

lineages

Boolean. Should the direct lineages be applied or curving, TRUE = curves, FALSE = lineages. Default = FALSE

pt_size

Numerical. What size should the cell points be. Default = 0.1

line_size

Numerical. What size should the lineage lines be. Default = 0.1

relevant

Should only pseudotime relevant cells be plotted. Default = TRUE

...

arguments to be passed to ggplot::geom_point

title

Character. Name the graph. Default = NULL

lab.clusters

Boolean. Whether the clusters within a lineage should be labelled, note this only works for lineages and not curves. Default = TRUE

Value

A ggplot of the reduced cellular embbedings and trajectories.