plotReducedDimWithTexts: plotReducedDimWithTexts

View source: R/sc.R

plotReducedDimWithTextsR Documentation

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.