Computes an HTML report from the Seurat workflow and returns the output SCE object with the computations stored in it.

seuratReport(
  inSCE,
  outputFile = NULL,
  outputDir = NULL,
  subtitle = "BUMC Single Cell Sequencing Core",
  authors = "Tianmu (Timo) Hu, Irzam Sarfraz",
  sce = NULL,
  biological.group = NULL,
  phenotype.groups = NULL,
  selected.markers = NULL,
  clustering.resolution = 0.8,
  variable.features = 2000,
  pc.count = 10,
  showSession = TRUE,
  pdf = TRUE
)

Arguments

inSCE: Input SingleCellExperiment object.
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.
outputDir: Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory.
subtitle: A character value specifying the subtitle to use in the Seurat report.
authors: A character value specifying the names of the authors to use in the Seurat report.
sce: A character value specifying the path of the input SingleCellExperiment object.
biological.group: A character value that specifies the name of the colData column to use as the main biological group in the seurat report for differential expression and grouping.
phenotype.groups: A character vector that specifies the names of the colData columns to use for differential expression in addition to the biological.group parameter.
selected.markers: A character vector specifying the user decided gene symbols of pre-selected markers that be used to generate gene plots in addition to the gene markers computed from differential expression.
clustering.resolution: A numeric value indicating the resolution to use with clustering. Default is 0.8.
variable.features: A numeric value indicating the number of top variable genes to identify in the seurat report. Default is 2000.
pc.count: A numeric value indicating the number of principal components to use in the analysis workflow. Default is 10.
showSession: A logical value indicating if session information should be displayed or not. Default is TRUE.
pdf: A logical value indicating if a pdf should also be generated for each figure in the report. Default is TRUE.

Value

A SingleCellExperiment object that has the seurat computations stored and can be used to interactively visualize the plots by importing in the singleCellTK user interface.