plot_density: Plot gene-weighted 2D kernel density

In powellgenomicslab/Nebulosa_Rv3: Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation

Description

Plot gene-weighted 2D kernel density

Usage

plot_density(
  object,
  features,
  slot = NULL,
  joint = FALSE,
  reduction = NULL,
  dims = c(1, 2),
  method = c("ks", "wkde"),
  adjust = 1,
  size = 1,
  shape = 16,
  combine = TRUE,
  pal = "viridis"
)

## S4 method for signature 'Seurat'
plot_density(
  object,
  features,
  slot = NULL,
  joint = FALSE,
  reduction = NULL,
  dims = c(1, 2),
  method = c("ks", "wkde"),
  adjust = 1,
  size = 1,
  shape = 16,
  combine = TRUE,
  pal = "viridis"
)

## S4 method for signature 'SingleCellExperiment'
plot_density(
  object,
  features,
  slot = NULL,
  joint = FALSE,
  reduction = NULL,
  dims = c(1, 2),
  method = c("ks", "wkde"),
  adjust = 1,
  size = 1,
  shape = 16,
  combine = TRUE,
  pal = "viridis"
)

Arguments

object	Seurat or SingleCellExperiment object
features	Features (e.g. genes) to visualize
slot	Type of data: counts ordata for Seurat objects and counts, logcounts, or normcounts for SingleCellExperiment objects
joint	Return joint density plot? By default FALSE
reduction	Name of the reduction to visualize. If not provided, last computed reduction is visualized
dims	Vector of length 2 specifying the dimensions to be plotted. By default, the first two dimensions are considered.
method	Kernel density estimation method: ks: Computes density using the kda function from the ks package. wkde: Computes density using a modified version of the kde2d function from the MASS package to allow weights. Bandwidth selection from the ks package is used instead.
adjust	Numeric value to adjust to bandwidth. Default: 1. Not available for ks method
size	Size of the geom to be plotted (e.g. point size)
shape	Shape of the geom to be plotted
combine	Create a single plot? If FALSE, a list with ggplot objects is returned
pal	String specifying the viridis color palette to use. Options: viridis magma cividis inferno plasma

Value

A scatterplot from a given reduction showing the gene-weighted density

Methods (by class)

• Seurat: Plot gene-weighted 2D kernel density

• SingleCellExperiment: Plot gene-weighted 2D kernel density

Author(s)

Jose Alquicira-Hernandez

Examples

data <- Seurat::pbmc_small
plot_density(data, "CD3E")

powellgenomicslab/Nebulosa_Rv3 documentation built on Sept. 18, 2020, 12:05 a.m.