Get runDEAnalysis .html report — reportDiffExp • singleCellTK

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

reportDiffExp(
  inSCE,
  study,
  useReducedDim,
  featureDisplay = NULL,
  output_file = NULL,
  output_dir = NULL
)

Arguments

inSCE: A SingleCellExperiment object containing the output from runDEAnalysis function
study: The specific analysis to visualize, used as analysisName argument when running differential expression.
useReducedDim: Specify an embedding for visualizing the relation ship between the conditions.
featureDisplay: The feature ID type to use for displaying. Should exists as a variable name of rowData. Default NULL use rownames of inSCE.
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.
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.

Saves the HTML report in the specified output directory.