geom_sc_wordcloud: geom_sc_wordcloud

View source: R/geom_sc_wordcloud.R

geom_sc_wordcloudR Documentation

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 May 31, 2024, 4:42 p.m.