rliger: plotByDatasetAndCluster – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

plotByDatasetAndCluster

Plot t-SNE coordinates of cells across datasets

Description

Generates two plots of all cells across datasets, one colored by dataset and one colored by cluster. These are useful for visually examining the alignment and cluster distributions, respectively. If clusters have not been set yet (quantileAlignSNF not called), will plot by single color for second plot. It is also possible to pass in another clustering (as long as names match those of cells).

Usage

plotByDatasetAndCluster(
  object,
  clusters = NULL,
  title = NULL,
  pt.size = 0.3,
  text.size = 3,
  do.shuffle = TRUE,
  rand.seed = 1,
  axis.labels = NULL,
  do.legend = TRUE,
  legend.size = 5,
  reorder.idents = FALSE,
  new.order = NULL,
  return.plots = FALSE,
  legend.fonts.size = 12
)

Arguments

`object`	`liger` object. Should call runTSNE or runUMAP before calling.
`clusters`	Another clustering to use for coloring second plot (must have same names as clusters slot) (default NULL).
`title`	Plot titles (list or vector of length 2) (default NULL).
`pt.size`	Controls size of points representing cells (default 0.3).
`text.size`	Controls size of plot text (cluster center labels) (default 3).
`do.shuffle`	Randomly shuffle points so that points from same dataset are not plotted one after the other (default TRUE).
`rand.seed`	Random seed for reproducibility of point shuffling (default 1).
`axis.labels`	Vector of two strings to use as x and y labels respectively.
`do.legend`	Display legend on plots (default TRUE).
`legend.size`	Size of legend on plots (default 5).
`reorder.idents`	logical whether to reorder the datasets from default order before plotting (default FALSE).
`new.order`	new dataset factor order for plotting. must set reorder.idents = TRUE.
`return.plots`	Return ggplot plot objects instead of printing directly (default FALSE).
`legend.fonts.size`	Controls the font size of the legend.

Value

List of ggplot plot objects (only if return.plots TRUE, otherwise prints plots to console).

Examples

## Not run: 
# ligerex (liger object), factorization complete
# get tsne.coords for normalized data
ligerex <- runTSNE(ligerex)
# plot to console
plotByDatasetAndCluster(ligerex)
# return list of plots
plots <- plotByDatasetAndCluster(ligerex, return.plots = TRUE)

## End(Not run)

rliger

Linked Inference of Genomic Experimental Relationships

v1.0.0

GPL-3

Authors

Joshua Welch [aut, ctb], Chao Gao [aut, ctb, cre], Jialin Liu [aut, ctb], Joshua Sodicoff [aut, ctb], Velina Kozareva [aut, ctb], Evan Macosko [aut, ctb], Paul Hoffman [ctb], Ilya Korsunsky [ctb], Robert Lee [ctb]

Initial release

2021-04-18