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 1.4.0 Index]