feature-grid-page: Create expression visualization for multiple selected...

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

Description

Users can select features and a dimension reduction to plot feature expression values.

Usage

add_feature_grid_page(dashboard, object, ...)

## S4 method for signature 'i2dashboard,missing'
add_feature_grid_page(
  dashboard,
  use_dimred,
  exprs_values,
  title = "Feature grid",
  page = "feature_grid_page",
  menu = "Tools"
)

## S4 method for signature 'i2dashboard,SingleCellExperiment'
add_feature_grid_page(
  dashboard,
  object,
  use_dimred,
  exprs_values,
  subset_row = NULL,
  ...
)

## S4 method for signature 'i2dashboard,Seurat'
add_feature_grid_page(
  dashboard,
  object,
  use_dimred,
  assay,
  slot = "data",
  subset_row = NULL,
  ...
)

Arguments

dashboard	An object of class i2dashboard.
object	A SingleCellExperiment object or a Seurat object.
...	Further parameters passed to the core function.
use_dimred	Coordinates of the reduced dimensions, used for the scatterplot (see Details).
exprs_values	Expression data of features of interest in rows and samples in columns (see Details).
title	The title of the page.
page	The name of the page to be added.
menu	(Optional) The name of the menu, under which the page should appear.
subset_row	A character vector (of feature names), a logical vector or numeric vector (of indices) specifying the features to use. The default of NULL will use all features.
assay	A character vector specifying which assay from object@assays to obtain expression values from.
slot	A character vector specifying the name of the slot in the assay.

Details

The parameters use_dimred, exprs_values (or assay) and group_by take different arguments depending on the class of object. In case no object is supplied (i2dashboard,missing-method), the parameters are expected to be of class data.frame or matrix. In case a SingleCellExperiment or Seurat object is supplied, the parameters are expected to be of class character, containing

• the name item(s) in reducedDims(object) or object@reductions,

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

• column names of colData(object) or [e-mail].

Value

An object of class i2dashboard.

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