dimred-comparison-page: Explore the effects of the parameters "theta" and...

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

Description

Creates a page with two tabs and a sidebar. The first tab generates the dimension reduction plot of the UMAP or t-SNE with the parameters set in the sidebar by clicking the "Generate plot" button. It is possible to save the scatterplot with its parameters to compare it with another parameters by clicking the button "Add plot for comparison". The second tab "Compare selected plots" contains a grid layout with the saved reduced dimensions. A list in the sidebar shows the saved plots and enables the deletion of plots.

Usage

add_dimred_comparison_page(dashboard, object, ...)

## S4 method for signature 'i2dashboard,missing'
add_dimred_comparison_page(
  dashboard,
  exprs_values,
  seed = NULL,
  calculateUMAP = list(),
  calculateTSNE = list(),
  page = "dimred_comparison_page",
  title = "Explore UMAP/t-SNE parameter",
  menu = "Tools"
)

## S4 method for signature 'i2dashboard,SingleCellExperiment'
add_dimred_comparison_page(
  dashboard,
  object,
  exprs_values = "logcounts",
  subset_row = NULL,
  ...
)

## S4 method for signature 'i2dashboard,SummarizedExperiment'
add_dimred_comparison_page(
  dashboard,
  object,
  exprs_values = "logcounts",
  subset_row = NULL,
  ...
)

## S4 method for signature 'i2dashboard,Seurat'
add_dimred_comparison_page(
  dashboard,
  object,
  assay = "RNA",
  assay_slot = "data",
  subset_row = NULL,
  ...
)

Arguments

dashboard	A i2dashboard.
object	An object of class Seurat, SingleCellExperiment or SummarizedExperiment.
...	Further parameters passed to the core function.
exprs_values	A numeric matrix of log-expression values where rows are features and columns are cells. Alternatively, a character indicating which assay of object to use.
seed	An integer vector, containing the random number generator (RNG) state for random number generation with set.seed().
calculateUMAP	A list with parameters passed on to scater::calculateUMAP()
calculateTSNE	A list with parameters passed on to scater::calculateTSNE()
page	The name of the page to be added.
title	The title of the page.
menu	The menu tab to which this page is subordinated. Default "Tools"
subset_row	An optional 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 specifying the assay (object@assays) to obtain expression values from. (Default: "RNA")
assay_slot	A character specifying the name of the data slot in the assay. (Default: "data")

Value

An object of class i2dashboard.

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