Render a pretty HTML QC report

Usage

render_qc_report(
  obj,
  metrics,
  status_df,
  save_dir = "qc_outputs",
  report_file = file.path(save_dir, "qc_report.html"),
  theme_bootswatch = "minty",
  self_contained = TRUE,
  sample_col = NULL,
  template = NULL,
  species = c("mouse", "human")
)

Arguments

obj: Seurat object (with qc_status in meta)
metrics: data.frame from calcQCmetrics()
status_df: data.frame from flagLowQuality()
save_dir: output dir for assets/plots (and where the Rmd will be copied)
report_file: output HTML path (default: file.path(save_dir, "qc_report.html"))
theme_bootswatch: Bootswatch theme name
self_contained: embed all assets into single HTML (TRUE)
sample_col: optional meta column for per-sample summaries
template: path to a .Rmd template; if NULL, copy bundled template to save_dir and use it
species: Character scalar, one of "mouse" or "human"