seaPiper Workflow output explorer — seapiper • seaPiper

seaPiper Workflow output explorer for the sea-snap pipeline

Usage

seapiper(
  pip,
  title = "Workflow output explorer",
  annot = NULL,
  cntr = NULL,
  tmod_res = NULL,
  tmod_dbs = NULL,
  primary_id = "PrimaryID",
  only_data = FALSE,
  debug_panel = FALSE
)

Arguments

pip: pipeline returned by load_de_pipeline
title: Name of the pipeline to display
annot: annotation returned by get_annot
cntr: contrasts list returned by get_contrasts
tmod_res: tmod results returned by get_tmod_res
tmod_dbs: tmod databases returned by get_tmod_dbs
primary_id: name of the column in the annotion data frame which corresponds to the primary gene identifier (including the row names of the contrasts results in the cntr object)
only_data: return the processed data and exit
debug_panel: show a debugging panel

Details

Launch a shiny app for viewing / exploring the results of a differential expression analysis performed in sea-snap.

Launching is much faster if the large objects (contrasts, tmod databases) do not need to be loaded each time the pipeline browser is started.

Examples

if(interactive()) {
  example_dir <- system.file("extdata/example_pipeline", package="Rseasnap")
  conf_f      <- file.path(example_dir, "DE_config.yaml")
  pip         <- load_de_pipeline(config_file = conf_f)
  pipeline_browser(pip)
}