plot.slingshot: Plots slingshot results

In connorhknight/IBRAP: Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)

Plots slingshot results

Description

Plots the results of the slingshot analysis using ggplots2

Usage

## S3 method for class '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.

connorhknight/IBRAP documentation built on March 9, 2023, 7:01 p.m.