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

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.