Get runCellQC .html report — reportCellQC • singleCellTK

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

reportCellQC(
  inSCE,
  output_file = NULL,
  output_dir = NULL,
  subTitle = NULL,
  studyDesign = NULL,
  useReducedDim = NULL
)

Arguments

inSCE: A SingleCellExperiment object containing the filtered count matrix with the output from runCellQC function
output_file: Character. The name of the generated file. If NULL/default then the output file name will be based on the name of the Rmarkdown template.
output_dir: Character. The name of the output directory to save the rendered file. If NULL/default the file is stored to the current working directory
subTitle: subtitle of the QC HTML report. Default is NULL.
studyDesign: Character. The description of the data set and experiment design. It would be shown at the top of QC HTML report. Default is NULL.
useReducedDim: Character. The name of the saved dimension reduction slot including cells from all samples in thenSingleCellExperiment object, Default is NULL

Value

.html file

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
if (FALSE) {
sce <- runCellQC(sce)
reportCellQC(inSCE = sce)
}