DimPlotWithTexts: DimPlotWithTexts

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

DimPlotWithTexts

Description

Directly output the dimension reduction plot with textual information.

Usage

DimPlotWithTexts(
  seu,
  markers,
  label = TRUE,
  pt.size = 0.5,
  reduction = "pca",
  point_alpha = 0.2,
  use_shadowtext = TRUE,
  bg.colour = "white",
  which.label = NULL,
  wc_alpha = 1,
  wcScale = 5,
  rot.per = 0.4,
  rad = NULL,
  sortBy = "avg_log2FC",
  scaleNumber = 2,
  decreasing = TRUE,
  geneNum = 50,
  base_ellipse = FALSE,
  base_dens = FALSE,
  random.order = FALSE,
  gene_name = FALSE,
  withggfx = NULL,
  ggfxParams = list(),
  withTitle = FALSE,
  args = list()
)

Arguments

seu	Seurat object
markers	results of FindAllMarkers()
label	plot label or not
pt.size	point size in plot
reduction	reduction method
point_alpha	point alpha
use_shadowtext	use shadowtext for wordcloud
bg.colour	shadowtext background color
which.label	which label to plot text
wc_alpha	alpha value for wordcloud
wcScale	scaling value for wordcloud
rot.per	ggwordcloud parameter
rad	named vector of size of each cluster
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
random.order	ggwordcloud parameter
gene_name	show gene names instead of textual information
withggfx	applying ggfx filters
ggfxParams	parameter list for ggfx
withTitle	whether to append title on wordcloud
args	parameters to passed to refseq

Details

The function accepts the Seurat object and marker gene information and output the reduced dimension plot with the textual information.

Value

single-cell plot with text annotation

See Also

plotReducedDimWithTexts

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