rliger: plotWordClouds – R documentation

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plotWordClouds

Generate word clouds and t-SNE plots

Description

Plots t-SNE coordinates of all cells by their loadings on each factor. Underneath it displays the most highly loading shared and dataset-specific genes, with the size of the marker indicating the magnitude of the loading.

It is recommended to call this function into a PDF due to the large number of plots produced.

Usage

plotWordClouds(
  object,
  dataset1 = NULL,
  dataset2 = NULL,
  num.genes = 30,
  min.size = 1,
  max.size = 4,
  factor.share.thresh = 10,
  log.fc.thresh = 1,
  pval.thresh = 0.05,
  do.spec.plot = TRUE,
  return.plots = FALSE,
  verbose = TRUE
)

Arguments

`object`	`liger` object. Should call runTSNE before calling.
`dataset1`	Name of first dataset (by default takes first two datasets for dataset1 and 2)
`dataset2`	Name of second dataset
`num.genes`	Number of genes to show in word clouds (default 30).
`min.size`	Size of smallest gene symbol in word cloud (default 1).
`max.size`	Size of largest gene symbol in word cloud (default 4).
`factor.share.thresh`	Use only factors with a dataset specificity less than or equalt to threshold (default 10).
`log.fc.thresh`	Lower log-fold change threshold for differential expression in markers (default 1).
`pval.thresh`	Upper p-value threshold for Wilcoxon rank test for gene expression (default 0.05).
`do.spec.plot`	Include dataset specificity plot in printout (default TRUE).
`return.plots`	Return ggplot objects instead of printing directly (default FALSE).
`verbose`	Print progress bar/messages (TRUE by default)

Value

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

Examples

## Not run: 
# ligerex (liger object based on in-memory datasets), factorization complete
ligerex <- quantile_norm(ligerex)
ligerex <- runTSNE(ligerex)
# pdf('word_clouds.pdf')
plotWordClouds(ligerex, num.genes = 20)
# dev.off()
# ligerex (liger object based on datasets in HDF5 format), factorization complete input
ligerex <- readSubset(ligerex, slot.use = "norm.data", max.cells = 5000)
plotWordClouds(ligerex, num.genes = 20)

## 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