geom_sc_wordcloud: geom_sc_wordcloud

In noriakis/wcGeneSummary: visualization and interpretation of textual information from omics summary data through network analysis

geom_sc_wordcloud

Description

Use ggplot_add to populate single-cell plot with textual information

Usage

geom_sc_wordcloud(
  markers,
  show_markers = NULL,
  gene_name = FALSE,
  p_val_adj_threshold = 0.05,
  keyType = "SYMBOL",
  rad = NULL,
  wc_alpha = 1,
  withTitle = FALSE,
  rot.per = 0.4,
  random.order = FALSE,
  use_shadowtext = TRUE,
  bg.colour = "white",
  wcScale = 4,
  args = list(),
  wcArgs = list(),
  sortBy = "avg_log2FC",
  scaleNumber = 2,
  decreasing = TRUE,
  geneNum = 50,
  base_ellipse = FALSE,
  base_dens = FALSE,
  withggfx = NULL,
  ggfxParams = list()
)

Arguments

markers	FindAllMarkers() results
show_markers	candidate clusters to be appear in plot, default to NULL, which means all the clusters are plotted
gene_name	show gene names instead of textual information
p_val_adj_threshold	default to 0.05, used in subsetting marker data frame using p_val_adj
keyType	key type of those listed in the markers. default to SYMBOL.
rad	named vector of radius for wordclouds. if specified, this value is used to define positions of annotation_custom.
wc_alpha	alpha value for word cloud
withTitle	whether to show title in each grob of wordcloud
rot.per	ggwordcloud parameter
random.order	ggwordcloud parameter
use_shadowtext	use shadowtext for wordcloud
bg.colour	the background color of shadowtext
wcScale	word cloud scaling factor
args	passed to refseq()
wcArgs	passed to ggwordcloud()
sortBy	default to avg_log2FC, "log10p" can be specified.
scaleNumber	scale the frequency of words by this number in 'gene_name'
decreasing	sort by decreasing order or not
geneNum	number of genes to be included in wordclouds
base_ellipse	if TRUE, wordclouds are placed based on stat_ellipse.
base_dens	if TRUE, wordclouds are placed based on density
withggfx	applying ggfx filters
ggfxParams	parameter list for ggfx

Details

Use layered approach to add wordclouds to the dimension reduction plots from single cell transcriptomics data. Use with 'ggsc'.

Value

ggplot

noriakis/wcGeneSummary documentation built on April 22, 2024, 7:12 a.m.