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Teal Module for RNA-seq Boxplot

Source: R/tm_g_boxplot.R
tm_g_boxplot.Rd

This module provides an interactive boxplot for RNA-seq gene expression analysis.

Usage 

tm_g_boxplot(
  label,
  mae_name,
  exclude_assays = character(),
  summary_funs = list(None = NULL, Mean = colMeans, Median = matrixStats::colMedians, Max
    = matrixStats::colMaxs),
  pre_output = NULL,
  post_output = NULL,
  .test = FALSE,
  transformators = list()
)

ui_g_boxplot(
  id,
  mae_name,
  summary_funs,
  pre_output,
  post_output,
  .test = FALSE
)

srv_g_boxplot(
  id,
  data,
  filter_panel_api,
  reporter,
  mae_name,
  exclude_assays,
  summary_funs,
  .test = FALSE
)

sample_tm_g_boxplot(.test = FALSE)

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.

summary_funs

(named list of functions or NULL)
functions which can be used in the the gene signatures. For modules that support also multiple genes without summary, NULL can be included to not summarize the genes but provide all of them.

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).

.test

(flag)
whether to display the internal structure of the plot for testing purposes.

transformators

(list of teal_transform_module) that will be applied to transform module's data input. To learn more check vignette("transform-input-data", package = "teal").

id

(string) the shiny module id.

data

(reactive)
reactive(<teal_data>) holding all the data sets provided during app initialization after going through the filters.

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_boxplot(): sets up the user interface.

  • srv_g_boxplot(): sets up the server with reactive graph.

  • sample_tm_g_boxplot(): sample module function.

Examples 

data <- teal_data(MAE = hermes::multi_assay_experiment)
app <- init(
  data = data,
  modules = modules(
    tm_g_boxplot(
      label = "boxplot",
      mae_name = "MAE"
    )
  )
)
#> Initializing tm_g_boxplot
if (interactive()) {
  shinyApp(app$ui, app$server)
}

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