plotWordClouds: Generate word clouds and t-SNE plots

In rliger: Linked Inference of Genomic Experimental Relationships

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

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
ligerex <- normalize(ligerex)
ligerex <- selectGenes(ligerex)
ligerex <- scaleNotCenter(ligerex)
ligerex <- optimizeALS(ligerex, k = 5, max.iter = 1)
ligerex <- quantile_norm(ligerex)
ligerex <- runTSNE(ligerex)
plotWordClouds(ligerex, do.spec.plot = FALSE)

rliger documentation built on Nov. 9, 2023, 1:07 a.m.