plot_density {Nebulosa} | R Documentation

## Plot gene-weighted 2D kernel density

### 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` or`data` 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.
`...` | Further scale arguments passed to scale_color_viridis_c 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 <- SeuratObject::pbmc_small
    plot_density(data, "CD3E")

[Package Nebulosa version 1.0.2 Index]