Teal Module for RNA-seq Quality Control — tm_g

This module adds quality flags, filters by genes and/or samples, normalizes AnyHermesData objects and provides interactive plots for RNA-seq gene expression quality control.

Usage

tm_g_quality(
  label,
  mae_name,
  exclude_assays = character(),
  pre_output = NULL,
  post_output = NULL
)

ui_g_quality(id, data, mae_name, pre_output, post_output)

srv_g_quality(id, data, filter_panel_api, reporter, mae_name, exclude_assays)

sample_tm_g_quality()

Arguments

label: (string)
menu item label of the module in the teal app.
mae_name: (string)
name of the MAE data used in the teal module.
exclude_assays: (character)
names of the assays which should not be included in choices in the teal module.
pre_output: (shiny.tag or NULL)
placed before the output to put the output into context (for example a title).
post_output: (shiny.tag or NULL)
placed after the output to put the output into context (for example the shiny::helpText() elements can be useful).
id: (string) the shiny module id.
data: (tdata)
tdata object which is automatically passed to the UI and server functions, holding all the data sets provided in the app initialization.
filter_panel_api: (FilterPanelAPI)
object describing the actual filter panel API.
reporter: (Reporter) object

Value

Shiny module to be used in the teal app.

Functions

ui_g_quality(): sets up the user interface.
srv_g_quality(): sets up the server with reactive graphs.
sample_tm_g_quality(): sample module function.

Examples

mae <- hermes::multi_assay_experiment
mae_data <- dataset("MAE", mae)
data <- teal_data(mae_data)
app <- init(
  data = data,
  modules = modules(
    tm_g_quality(
      label = "Quality Control",
      mae_name = "MAE"
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

# Alternatively you can run the sample module with this function call:
if (interactive()) {
  sample_tm_g_quality()
}