generate_qc_report: Generate a QC report from a SingleCellExperiment object

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

Generate a QC report from a SingleCellExperiment object

Description

Generate a QC report from a SingleCellExperiment object

Usage

generate_qc_report(
  library_id,
  unfiltered_sce,
  filtered_sce = NULL,
  processed_sce = NULL,
  report_template = NULL,
  extra_params = NULL,
  output = NULL,
  ...
)

Arguments

library_id	The name of the library_id for report headers
unfiltered_sce	A SingleCellExperiment object that the report will describe
filtered_sce	An optional filtered single cell experiment derived from first
processed_sce	An optional single cell experiment that has been normalized and contains PCA and UMAP embeddings
report_template	An optional path to a template rmd file to be rendered, if no file is provided, the default 'qc_report.rmd' file present in the package will be used.
extra_params	An optional named list of additional parameters to use when rendering the provided rmd file.
output	The output file path that will be created. If the file name does not include an extension, ".html" will be added automatically. Any directories in the path will be created as needed.
...	Additional arguments to pass to rmarkdown::render()

Value

The full path of the output file

Examples

## Not run: 
generate_qc_report("Library 1", my_sce, output = "reports/sample1_report.html")

## End(Not run)

AlexsLemonade/scpcaTools documentation built on July 12, 2024, 8:34 a.m.