Get diffAbundanceFET .html report — reportDiffAbundanceFET • singleCellTK

A function to generate .html Rmarkdown report containing the visualizations of the diffAbundanceFET function output

reportDiffAbundanceFET(
  inSCE,
  cluster,
  variable,
  control,
  case,
  analysisName,
  output_dir = ".",
  output_file = "DifferentialAbundanceFET_Report",
  pdf = FALSE,
  showSession = TRUE
)

Arguments

inSCE: A SingleCellExperiment object.
cluster: A single character, specifying the name to store the cluster label in colData.
variable: A single character, specifying the name to store the phenotype labels in colData.
control: character. Specifying one or more categories that can be found in the vector specified by variable.
case: character. Specifying one or more categories that can be found in the vector specified by variable.
analysisName: A single character. Will be used for naming the result table, which will be saved in metadata slot.
output_dir: name of the output directory to save the rendered file. If NULL the file is stored to the current working directory. Default NULL.
output_file: name of the generated file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.
pdf: A logical value indicating if a pdf should also be generated for each figure in the report. Default is TRUE.
showSession: A logical value indicating if session information should be displayed or not. Default is TRUE.

Value

An HTML file of the report will be generated at the path specified in the arguments.