generateShinyApp {bulkAnalyseR}

Generate all files required for an autonomous shiny app

Description

This function creates an app.R file and all required objects to run the app in .rda format in the target directory. A basic argument check is performed to avoid input data problems. The app directory is standalone and can be used on another platform, as long as bulkAnalyseR is installed there. It is recommended to run preprocessExpressionMatrix before this function.

Usage

generateShinyApp(
  shiny.dir = "shiny_bulkAnalyseR",
  app.title = "Visualisation of RNA-Seq data",
  theme = "flatly",
  modality = "RNA",
  expression.matrix,
  metadata,
  organism = NA,
  org.db = NA,
  panels.default = c("Landing", "SampleSelect", "QC", "GRN", "DE", "DEplot", "DEsummary",
    "Enrichment", "GRNenrichment", "Cross", "Patterns"),
  panels.extra = tibble::tibble(name = NULL, UIfun = NULL, UIvars = NULL, serverFun =
    NULL, serverVars = NULL),
  data.extra = list(),
  packages.extra = c(),
  cis.integration = tibble::tibble(reference.expression.matrix = NULL, reference.org.db =
    NULL, reference.coord = NULL, comparison.coord = NULL, reference.table.name = NULL,
    comparison.table.name = NULL),
  trans.integration = tibble::tibble(reference.expression.matrix = NULL, reference.org.db
    = NULL, comparison.expression.matrix = NULL, comparison.org.db = NULL,
    reference.table.name = NULL, comparison.table.name = NULL),
  custom.integration = tibble::tibble(reference.expression.matrix = NULL,
    reference.org.db = NULL, comparison.table = NULL, reference.table.name = NULL,
    comparison.table.name = NULL)
)

Arguments

shiny.dir

directory to store the shiny app; if a non-empty directory with that name already exists an error is generated

app.title

title to be displayed within the app

theme

shiny theme to be used in the app; default is 'flatly'

modality

name of the modality, or a vector of modalities to be included in the app

expression.matrix

the expression matrix; rows correspond to genes and columns correspond to samples; usually preprocessed by preprocessExpressionMatrix; a list (of the same length as modality) can be provided if #' length(modality) > 1

metadata

a data frame containing metadata for the samples contained in the expression.matrix; must contain at minimum two columns: the first column must contain the column names of the expression.matrix, while the last column is assumed to contain the experimental conditions that will be tested for differential expression; a list (of the same length as modality) can be provided if #' length(modality) > 1

organism

organism name to be passed on to gprofiler2::gost; organism names are constructed by concatenating the first letter of the name and the family name; default is NA - enrichment is not included to ensure compatibility with datasets that have non-standard gene names; a vector (of the same length as modality) can be provided if length(modality) > 1

org.db

database for annotations to transform ENSEMBL IDs to gene names; a list of bioconductor packaged databases can be found with BiocManager::available("^org\."); default in NA, in which case the row names of the expression matrix are used directly - it is recommended to provide ENSEMBL IDs if the database for your model organism is available; a vector (of the same length as modality) can be provided if length(modality) > 1

panels.default

argument to control which of the default panels will be included in the app; default is all, but the enrichment panel will not appear unless organism is also supplied; note that the 'DE' panel is required for 'DEplot', 'DEsummary', 'Enrichment', and 'GRNenrichment'; a list (of the same length as modality) can be provided if length(modality) > 1

panels.extra, data.extra, packages.extra

functionality to add new user-created panels to the app to extend functionality or change the default behaviour of existing panels; a data frame of the modality, panel UI and server names and default parameters should be passed to panels.extra (see example); the names of any packages required should be passed to the packages.extra argument; extra data should be a single list and passed to the data.extra argument

cis.integration

functionality to integrate extra cis-regulatory information into GRN panel. Tibble containing names of reference expression matrix, tables of coordinates for elements corresponding to rows of reference expression matrix (reference.coord), tables of coordinates to compare against reference.coord (comparison.coord) and names for comparison tables. See vignettes for more details about inputs.

trans.integration

functionality to integrate extra trans-regulatory information into GRN panel. Tibble containing names of reference expression matrix, (reference.expression.matrix), comparison expression matrix (comparison.expression.matrix). Organism database names for each expression matrix and names for each table are also required. See vignettes for more details about inputs.

custom.integration

functionality to integrate custom information related to rows of reference expression matrix. Tibble containing names of reference expression matrix, tables (comparison.table) with Reference_ID and Reference_Name (matching ENSEMBL and NAME columns of reference organism database) and Comparison_ID and Comparison_Name plus a Category column containing extra information. Names for the reference expression matrix and comparison table (comparison.table.name) are also required. See vignettes for more details about inputs.

Value

The path to shiny.dir (invisibly).

Examples

expression.matrix.preproc <- as.matrix(read.csv(
  system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"), 
  row.names = 1
))
metadata <- data.frame(
  srr = colnames(expression.matrix.preproc), 
  timepoint = rep(c("0h", "12h", "36h"), each = 2)
)
app.dir <- generateShinyApp(
  shiny.dir = paste0(tempdir(), "/shiny_Yang2019"),
  app.title = "Shiny app for the Yang 2019 data",
  modality = "RNA",
  expression.matrix = expression.matrix.preproc,
  metadata = metadata,
  organism = "mmusculus",
  org.db = "org.Mm.eg.db"
)
# runApp(app.dir)

# Example of an app with a second copy of the QC panel
app.dir.qc2 <- generateShinyApp(
  shiny.dir = paste0(tempdir(), "/shiny_Yang2019_QC2"),
  app.title = "Shiny app for the Yang 2019 data",
  expression.matrix = expression.matrix.preproc,
  metadata = metadata,
  organism = "mmusculus",
  org.db = "org.Mm.eg.db",
  panels.extra = tibble::tibble(
    name = "RNA2",
    UIfun = "modalityPanelUI", 
    UIvars = "'RNA2', metadata[[1]], NA, 'QC'", 
    serverFun = "modalityPanelServer", 
    serverVars = "'RNA2', expression.matrix[[1]], metadata[[1]], anno[[1]], NA, 'QC'"
  )
)
# runApp(app.dir.qc2)

# clean up tempdir
unlink(paste0(normalizePath(tempdir()), "/", dir(tempdir())), recursive = TRUE)