Plot gene-weighted density — plot_gw

Quickly visualize expression gene-weighted density of one or more features based on Nebulosa.

Usage

plot_gw_density(
  data,
  features,
  reduction = "umap.harmony",
  size = 0.2,
  pal = "magma",
  ncol = 2,
  joint = FALSE,
  combine = TRUE,
  ...
)

Arguments

data: A Seurat object with a "harmony" reduction and UMAP computed on it.
features: Character vector of feature names to plot.
reduction: Name of the reduction to use for plotting (default "umap.harmony").
size: Size of the geom to be plotted (e.g. point size)
pal: Choose from Nebulosa's palettes, e.g. "magma", "inferno", "plasma", "viridis", "cividis".
ncol: Number of columns in the output layout (default 2).
joint: Return joint density plot? By default FALSE
combine: Passed to Nebulosa::plot_density().
...: Additional arguments passed to Nebulosa::plot_density().

Value

A patchwork object arranging density plots in a grid.

Examples

if (FALSE) { # \dontrun{
# Assuming 'obj' is a Seurat object with harmony UMAP
library(Seurat)
library(Nebulosa)
library(patchwork)
data <- SeuratObject::pbmc_small
plot_gw_density(data, c("CD3D", "CD3E"),
                reduction = "tsne", ncol = 2)
# joint density
plot_gw_density(data, c("CD3D", "CD3E"),
                reduction = "tsne",
                joint = TRUE, combine = FALSE)
} # }