shiny_report: Shiny report

In MonashBioinformaticsPlatform/varistran: Variance Stabilizing Transformations appropriate for RNA-Seq expression data

Shiny report

Description

Produce an interactive Shiny report showing diagnostic plots of transformed counts.

Usage

shiny_report(
  y = NULL,
  counts = NULL,
  sample_labels = NULL,
  feature_labels = NULL,
  prefix = ""
)

Arguments

y	A matrix of exprssion levels, such as a transformed counts matrix.
counts	Original counts.
sample_labels	Optional. Sample names.
feature_labels	Optional. Feature names.
prefix	Optional, to facilitate use as a component of a larger Shiny app. Inputs and outputs are given this prefix.

Value

A shiny.appobj.

Either y or counts or both must be given.

Used interactively, the shiny report runs immediately. Otherwise it can be launched by print()-ing it. A call to this function can also be the last line in an app.R file in a Shiny app directory.

Author(s)

Paul Harrison

Examples

# Generate some random data.
means <- runif(100,min=0,max=1000)
counts <- matrix(rnbinom(1000, size=1/0.01, mu=rep(means,10)), ncol=10)

y <- varistran::vst(counts)
if (interactive())
    varistran::shiny_report(y, counts)

MonashBioinformaticsPlatform/varistran documentation built on June 9, 2025, 8:36 a.m.