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

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

reportSeuratFeatureSelection(
  inSCE,
  variable.features = 2000,
  runHVG = TRUE,
  plotHVG = TRUE,
  outputFile = NULL,
  outputPath = NULL,
  subtitle = NULL,
  authors = NULL,
  showSession = FALSE,
  pdf = FALSE,
  forceRun = FALSE
)

Arguments

inSCE

Input SingleCellExperiment object.

variable.features

A numeric value indicating the number of top variable features to identify. Default 2000.

runHVG

A logical value indicating if the feature selection algorithm should be run or not. Default TRUE.

plotHVG

A logical value indicating if the mean-to-variance plot of the top variable feature should be visualized or not. 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 FALSE.

Value

A SingleCellExperiment object with computations stored.