Introduction
teal.modules.hermes is a package implementing a number
of teal modules for the exploration of RNA-sequencing
counts data. In addition to predefined modules,
teal.modules.hermes enables quick and easy ad-hoc module
creation.
Ad-hoc module example
Let’s assume you have a function awesome_plot() which
takes a count matrix and makes an awesome plot out of it. Now you would
like to make a Shiny app where you can filter patients, samples, select
the experiment out of your MultiAssayExperiment (MAE),
select the count matrix from the experiment, etc. Nothing is easier than
that with teal.modules.hermes! We show you below how to
quickly spin up your UI, server and put them together into a nice little
app.
UI function
In teal.modules.hermes we provide modules that make the
experiment and assay selection super easy, see here for the UI part:
ui <- function(id, mae_name) {
ns <- NS(id)
teal.widgets::standard_layout(
encoding = uiOutput(ns("encoding_ui")),
output = plotOutput(ns("awesome_plot"))
)
}Server function
Similarly for the server we use the modules, and call then our awesome plotting function.
srv <- function(input,
output,
session,
data,
filter_panel_api,
mae_name) {
output$encoding_ui <- renderUI({
div(
experimentSpecInput(session$ns("experiment"), data, mae_name),
assaySpecInput(session$ns("assay"))
)
})
experiment <- experimentSpecServer(
"experiment",
data = data,
filter_panel_api = filter_panel_api,
mae_name = mae_name,
name_annotation = NULL # If you have a gene name column in your rowData, can specify here.
)
assay <- assaySpecServer("assay", experiment$assays)
output$awesome_plot <- renderPlot({
data <- experiment$data()
assay <- assay()
req(assay %in% SummarizedExperiment::assayNames(data))
counts <- SummarizedExperiment::assay(data, assay)
df <- data.frame(gene = rownames(counts), counts = rowSums(counts))
df <- na.omit(df[order(df$counts, decreasing = TRUE), ])
df$gene <- factor(df$gene, levels = df$gene)
df <- df[1:10, ]
ggplot(df, aes(x = gene, y = counts)) +
geom_col() +
theme(axis.text.x = element_text(angle = 90))
})
}App function
Now let’s assume you want to spin up your app for an MAE.
awesome_app <- function(mae, label = "My awesome app") {
mae_name <- "MAE"
data <- teal_data(MAE = hermes::lapply(mae, hermes::HermesData))
app <- init(
data = data,
modules = teal::modules(
module(
label = label,
server = srv,
server_args = list(mae_name = mae_name),
ui = ui,
ui_args = list(mae_name = mae_name),
datanames = mae_name
)
)
)
shinyApp(app$ui, app$server)
}