RidgePlot: Single cell ridge plot

In satijalab/seurat: Tools for Single Cell Genomics

Single cell ridge plot

Description

Draws a ridge plot of single cell data (gene expression, metrics, PC scores, etc.)

Usage

RidgePlot(
  object,
  features,
  cols = NULL,
  idents = NULL,
  sort = FALSE,
  assay = NULL,
  group.by = NULL,
  y.max = NULL,
  same.y.lims = FALSE,
  log = FALSE,
  ncol = NULL,
  slot = deprecated(),
  layer = "data",
  stack = FALSE,
  combine = TRUE,
  fill.by = "feature"
)

Arguments

object	Seurat object
features	Features to plot (gene expression, metrics, PC scores, anything that can be retreived by FetchData)
cols	Colors to use for plotting
idents	Which classes to include in the plot (default is all)
sort	Sort identity classes (on the x-axis) by the average expression of the attribute being potted, can also pass 'increasing' or 'decreasing' to change sort direction
assay	Name of assay to use, defaults to the active assay
group.by	Group (color) cells in different ways (for example, orig.ident)
y.max	Maximum y axis value
same.y.lims	Set all the y-axis limits to the same values
log	plot the feature axis on log scale
ncol	Number of columns if multiple plots are displayed
slot	Slot to pull expression data from (e.g. "counts" or "data")
layer	Layer to pull expression data from (e.g. "counts" or "data")
stack	Horizontally stack plots for each feature
combine	Combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot
fill.by	Color violins/ridges based on either 'feature' or 'ident'

Value

A patchworked ggplot object if combine = TRUE; otherwise, a list of ggplot objects

Examples

data("pbmc_small")
RidgePlot(object = pbmc_small, features = 'PC_1')

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.