modeGating {iSEE}R Documentation

App pre-configured to link multiple feature assay plots

Description

App pre-configured to link multiple feature assay plots

Usage

modeGating(se, features, featAssayMax = max(2, nrow(features)), ...,
  plot_width = 4)

Arguments

se

An object that coercible to SingleCellExperiment

features

data.frame with columns named x and y that define the features on the axes of the linked plots. Plots are serially linked from the first row to the last.

featAssayMax

Maximal number of feature assay plots in the app.

...

Additional arguments passed to iSEE.

plot_width

The grid width of linked plots (numeric vector of length either 1 or equal to nrow(features)

Value

A Shiny App preconfigured with multiple chain-linked feature expression plots is launched for interactive data exploration of the SingleCellExperiment / SummarizedExperiment object

Examples

library(scRNAseq)
data(allen)
class(allen)

# Example data ----

library(scater)
sce <- as(allen, "SingleCellExperiment")
counts(sce) <- assay(sce, "tophat_counts")
sce <- normalize(sce)


# Select top variable genes ----

plot_count <- 6
rv <- rowVars(logcounts(sce))
top_var <- head(order(rv, decreasing = TRUE), plot_count*2)
top_var_genes <- rownames(sce)[top_var]

plot_features <- data.frame(
    x = head(top_var_genes, plot_count),
    y = tail(top_var_genes, plot_count),
    stringsAsFactors = FALSE
 )

# launch the app itself ----

app <- modeGating(sce, features = plot_features, featAssayMax = 6)
if (interactive()) {
  shiny::runApp(app, port = 1234)
}

[Package iSEE version 1.0.1 Index]