Explore Data {scran}R Documentation

Shiny app for explorative data analysis

Description

Generate an interactive Shiny app to explore gene expression patterns in single-cell data

Usage

exploreData(x, cell.data, gene.data, red.dim, run=TRUE)

Arguments

x

A numeric matrix of expression values to be visualized.

cell.data

A data frame of cell information, where each row corresponds to a column of x.

gene.data

A data frame of gene information, where each row corresponds to a row of x.

red.dim

A numeric matrix with two colums, specifying the reduced-dimension coordinates for each cell.

run

A logical scalar specifying whether the app should be run immediately.

Details

Note that this function is deprecated; we suggest using the iSEE package for data exploration instead.

This function will return a Shiny app object that can be run with runApp. The app allows the user to interactively explore gene expression patterns in single-cell RNA-seq data. Explorative analysis is focused on comparing gene exression between different groups of cells, as defined by the covariates of cell.data.

Three plots are shown in the app:

Several options are available within the app:

“Color by”:

Covariate to be used for coloring the first scatter plot.

“Group by”:

Covariate with which expression values are grouped in the boxplots.

In addition, the gene.data data frame is rendered as an interactive table using the JavaScript library DataTable. This allows the user to subset/search the feature data and select a gene by clicking on the corresponding row.

Value

If run=FALSE, a Shiny app object is returned, which can be run with runApp. If run=TRUE, a Shiny app object is created and run.

Author(s)

Karsten Bach

See Also

runApp,

Examples

# Set up example data
example(SingleCellExperiment)
cell.data <- DataFrame(stuff=sample(LETTERS, ncol(sce), replace=TRUE))
gene.data <- DataFrame(lengths=runif(nrow(sce)))

# Mocking up  some reduced dimensions.
pca <- prcomp(t(exprs(sce)))
red.dim <- pca$x[,1:2]

# Creating the app object.
app <- exploreData(exprs(sce), cell.data, gene.data, red.dim, run=FALSE)
if (interactive()) { shiny::runApp(app) }

## Not run: # Running directly from the function.
saved <- exploreData(x, cell.data, gene.data, red.dim)

## End(Not run)

[Package scran version 1.8.4 Index]