rliger (version 1.0.1)

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
)

Value

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

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)

Examples

# \donttest{
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)
# }