Renders a component containing a bubbleplot with optional selection options

bubbleplot(dashboard, object, ...)

# S4 method for i2dashboard,missing
bubbleplot(
  dashboard,
  x,
  y,
  size,
  colour_by = NULL,
  labels = NULL,
  title = NULL,
  x_title = NULL,
  y_title = NULL,
  plot_title = NULL
)

# S4 method for i2dashboard,SingleCellExperiment
bubbleplot(
  dashboard,
  object,
  from = c("colData", "rowData", "reducedDim"),
  x = NULL,
  y = NULL,
  size = NULL,
  colour_by = NULL,
  use_dimred = NULL,
  ...
)

# S4 method for i2dashboard,Seurat
bubbleplot(
  dashboard,
  object,
  from = c("meta.data", "meta.features", "embedding"),
  x = NULL,
  y = NULL,
  size = NULL,
  colour_by = NULL,
  use_dimred = NULL,
  assay = "RNA",
  slot = NULL,
  subset_row = NULL,
  ...
)

Arguments

dashboard

An object of class i2dash::i2dashboard.

object

An object of class Seurat::Seurat or SingleCellExperiment::SingleCellExperiment.

x

Data that will be mapped to the x-axis (see Details).

y

Data that will be mapped to the y-axis (see Details).

size

Numeric or factorial values that describe the size of the bubbles.

colour_by

Numeric or factorial values that will be used for colouring.

labels

An optional vector with sample names. A dropdown menu for colouring by label will be provided.

title

The title of the components junk.

x_title

An optional title of the x-axis. If not provided the column names from x are used instead.

y_title

An optional title of the y-axis. If not provided the column names from y are used instead.

plot_title

An optional title of the plot.

from

A character specifying where to obtain the data from object (see Details).

use_dimred

A character vector indicating the reduced dimension to use from "object" (see Details).

assay

A character defining the assay of object.

Value

A string containing markdown code for the rendered component

Details

The parameters x, y, size, colour_by, use_dimred and assay take different arguments depending on the class of object. In case the i2dashboard,missing-method, the parameters x, y, size, colour_by are expected to be of class data.frame or matrix. The parameters x, y and size can also be numeric vectors. The parameters from, use_dimred, assay and slot can be ignored. In case the i2dashboard,SingleCellExperiment-method, the parameters are expected to be of class character:

  • the parameter from can be either "colData", "rowData" or "reducedDim"

  • use_dimred the name of an item in reducedDims(object)

In case of the i2dashboard,Seurat-method, the parameters are expected to be of class character:

  • the parameter from can be either "meta.data" for sample metadata, "meta.feature" for feature metadata, "embedding" for a dimension reduction

  • reduction the name of an item in object@reductions

  • assay a valid assay name from names(object@assays)

In both cases, x, y, colour_by take column names of from.