bubbleplot: Renders a component containing a bubbleplot with optional...

In loosolab/i2dash.scrnaseq: Iterative and Interactive Dashboards for single-cell RNA-sequencing data

Description

Renders a component containing a bubbleplot with optional selection options

Usage

bubbleplot(dashboard, object, ...)

## S4 method for signature '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 signature '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 signature '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.

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.

Value

A string containing markdown code for the rendered component

loosolab/i2dash.scrnaseq documentation built on Jan. 1, 2021, 8:23 a.m.