reportSeuratDimRed: Generates an HTML report for Seurat Dimensionality Reduction...

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Generates an HTML report for Seurat Dimensionality Reduction and returns the SCE object with the results computed and stored inside the object.

Description

Generates an HTML report for Seurat Dimensionality Reduction and returns the SCE object with the results computed and stored inside the object.

Usage

reportSeuratDimRed(
  inSCE,
  pc.count = 50,
  runDimRed = TRUE,
  plotJackStraw = FALSE,
  plotElbowPlot = TRUE,
  plotHeatmaps = TRUE,
  outputFile = NULL,
  outputPath = NULL,
  subtitle = NULL,
  authors = NULL,
  showSession = FALSE,
  pdf = FALSE,
  forceRun = TRUE
)

Arguments

inSCE	Input SingleCellExperiment object.
pc.count	A numeric value indicating the number of principal components to compute. Default is 50.
runDimRed	A logical value indicating if dimenionality reduction should be computed. Default TRUE.
plotJackStraw	A logical value indicating if JackStraw plot should be visualized. Default FALSE.
plotElbowPlot	A logical value indicating if ElbowPlot should be visualized. Default TRUE.
plotHeatmaps	A logical value indicating if heatmaps should be visualized. Default TRUE.
outputFile	Specify the name of the generated output HTML file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.
outputPath	Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory. Default NULL.
subtitle	A character value specifying the subtitle to use in the report. Default NULL.
authors	A character value specifying the names of the authors to use in the report. Default NULL.
showSession	A logical value indicating if session information should be displayed or not. Default is FALSE.
pdf	A logical value indicating if a pdf should also be generated for each figure in the report. Default is FALSE.
forceRun	A logical value indicating if all computations previously computed should be re-calculated regardless if these computations are available in the input object. Default is TRUE.

Value

A SingleCellExperiment object with computations stored.

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.