modeGating {iSEEu} | R Documentation

## 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)
    }

[Package iSEEu version 1.4.0 Index]