plotReducedDimWithTexts: plotReducedDimWithTexts

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

plotReducedDimWithTexts

Description

Directly output the dimension reduction plot with textual information.

Usage

plotReducedDimWithTexts(
  sce,
  marker.info,
  colour_by = "label",
  point_alpha = 0.4,
  use_shadowtext = TRUE,
  bg.colour = "white",
  which.label = NULL,
  wc_alpha = 1,
  wcScale = 5,
  rot.per = 0.4,
  rad = NULL,
  top = 5,
  gene_name = FALSE,
  withggfx = NULL,
  ggfxParams = list(),
  sortBy = "summary.logFC",
  scaleNumber = 2,
  decreasing = TRUE,
  geneNum = 50,
  random.order = FALSE,
  dimred = "PCA",
  base_ellipse = FALSE,
  base_dens = FALSE,
  withTitle = FALSE,
  args = list()
)

Arguments

sce	sce object
marker.info	results of findMarkers()
colour_by	colorize by this label
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
top	Top-top genes are included
gene_name	show gene names instead of textual information
withggfx	applying ggfx filters
ggfxParams	parameter list for ggfx
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
random.order	ggwordcloud parameter
dimred	dimension reduction method
base_ellipse	if TRUE, wordclouds are placed based on stat_ellipse.
base_dens	if TRUE, wordclouds are placed based on density
withTitle	whether to append title on wordcloud
args	parameters to passed to refseq

Details

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

Value

single-cell plot with text annotation

See Also

DimPlotWithTexts

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.