SingleViolinIPlot: Violin plot by identity

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Violin plot by identity

Description

Violin plot by identity

Usage

SingleViolinIPlot(
  data,
  idents,
  hl = NULL,
  title = NULL,
  sort = FALSE,
  y.max = NULL,
  adjust = 1,
  pt.size = 1,
  pt.shape = 20,
  seed.use = 42,
  log = FALSE,
  color = NULL,
  color_dark = NULL,
  nsel = 1,
  ncells = NULL,
  pct.cells = NULL
)

Arguments

data	Data to plot
idents	Idents to use
hl	Factor used to highlight specific idents via fill, alpha, and color geoms.
title	Plot title
sort	Sort identity classes (on the x-axis) by the average expression of the attribute being potted
y.max	Maximum Y value to plot
adjust	Adjust parameter for geom_violin
pt.size	size parameter for geom_jitter
pt.shape	shape parameter for geom_jitter
seed.use	Random seed to use. If NULL, don't set a seed
log	plot Y axis on log scale
color	Colors to use for fill with length equal to one less than length(levels(hl)). The last level of hl is filled with gray.
color_dark	Darker versions of color used for points and lines.
nsel	Number of selected idents. Default is 1.
ncells	Vector specifying number of cells in each levels(idents). If specified, an annotated bar plot is drawn to indicate number of cells.
pct.cells	Vector specifying percent of cells that express the marker, once for each levels(idents). If specified, an annotated bar plot is drawn.

Value

A ggplot-based Violin-by-Identity plot

hms-dbmi/drugseqr documentation built on Feb. 15, 2024, 10:38 p.m.