plotVolcanoApp {bigPint} | R Documentation

## Plot interactive volcano plots

### Description

Plot interactive volcano plots.

### Usage

    plotVolcanoApp(
      data = data,
      dataMetrics = dataMetrics,
      dataSE = NULL,
      option = c("hexagon", "allPoints"),
      pointColor = "orange"
    )

### Arguments

`data` | DATA FRAME | Read counts
`dataMetrics` | LIST | Differential expression metrics. This object must contain one column named "logFC" and one column named "PValue".
`dataSE` | SUMMARIZEDEXPERIMENT | Summarized experiment format that can be used in lieu of data; default NULL
`option` | CHARACTER STRING ["hexagon" | "allPoints"] | The background of plot; default "hexagon"
`pointColor` | CHARACTER STRING | Color of overlaid points on scatterplot matrix; default "orange"

### Value

A Shiny application that shows a volcano plot and allows users to overlay genes depending on two values, usually a statistical value (such as P-value) and a magnitude change value (such as log fold change). The user can download a file that contains the gene IDs that pass these thresholds.

### Examples

    # The first pair of examples use data and dataMetrics objects as input.
    # The last pair of examples create the same plots now using the
    # SummarizedExperiment (i.e. dataSE) object input.

    # Example 1: Create interactive volcano plot of logged data using hexagon
    # bins for the background.

    data(soybean_cn_sub)
    data(soybean_cn_sub_metrics)
    app <- plotVolcanoApp(data = soybean_cn_sub,
        dataMetrics = soybean_cn_sub_metrics)
    if (interactive()) {
        shiny::runApp(app)
    }

    # Example 2: Create interactive volcano plot of logged data using points for
    # the background.

    app <- plotVolcanoApp(data = soybean_cn_sub,
        dataMetrics = soybean_cn_sub_metrics, option = "allPoints",
        pointColor = "magenta")
    if (interactive()) {
        shiny::runApp(app)
    }

    # Below is the same pair of examples, only now using the
    # SummarizedExperiment (i.e. dataSE) object as input.

    # Example 1: Create interactive volcano plot of logged data using hexagon
    # bins for the background.

    ## Not run:
    data(se_soybean_cn_sub)
    app <- plotVolcanoApp(dataSE = se_soybean_cn_sub)
    if (interactive()) {
        shiny::runApp(app)
    }

    ## End(Not run)

    # Example 2: Create interactive volcano plot of logged data using points for
    # the background.

    ## Not run:
    app <- plotVolcanoApp(dataSE = se_soybean_cn_sub, option = "allPoints",
        pointColor = "magenta")
    if (interactive()) {
        shiny::runApp(app)
    }

    ## End(Not run)

[Package bigPint version 1.4.0 Index]