modeGating: App pre-configured to link multiple feature assay plots

In iSEE/iSEEu: iSEE Universe

App pre-configured to link multiple feature assay plots

Description

This mode launches a Shiny App preconfigured with multiple chain-linked feature expression plots for interactive data exploration of the SingleCellExperiment or SummarizedExperiment object.

Usage

modeGating(se, features, plotAssay = NA_character_, ..., plotWidth = 4)

Arguments

se	An object that coercible to SingleCellExperiment-class
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.
plotAssay	The assay (one of assayNames(se)) to use for the plots (character vector of length either 1 or equal to nrow(features)).
...	Additional arguments passed to iSEE().
plotWidth	The grid width of linked plots (numeric vector of length either 1 or equal to nrow(features)

Value

A Shiny app object is returned.

Examples

library(scRNAseq)

# Example data ----
sce <- ReprocessedAllenData(assays="tophat_counts")
class(sce)

library(scater)
sce <- logNormCounts(sce, exprs_values="tophat_counts")

# Select top variable genes ----

plot_count <- 6
rv <- rowVars(assay(sce, "tophat_counts"))
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)
if (interactive()) {
  shiny::runApp(app, port=1234)
}

iSEE/iSEEu documentation built on Oct. 11, 2024, 9:20 a.m.