plotOpenSignal {GenomicDistributions} | R Documentation

## The function plotOpenSignal visualizes the signalMatrix obtained from calcOpenSignal.

### Description

The function plotOpenSignal visualizes the signalMatrix obtained from calcOpenSignal.

### Usage

    plotOpenSignal(
      openRegionSummary,
      plotType = "barPlot",
      cellGroup = NA,
      cellTypeMetadata = NA,
      colorScheme = c("#E31A1C", "#666666", "#B3DE69", "#A65628", "#33A02C", "#E6AB02",
        "#F0027F", "#FDC086", "#FFFF99", "#B3E2CD", "#B3CDE3", "#66A61E", "#F4CAE4",
        "#80B1D3", "#FFED6F", "#B15928", "#999999")
    )

### Arguments

`openRegionSummary` | Output list from `calcOpenSignal` function.
`plotType` | Options are: "jitter" - jitter plot with box plot on top, "boxPlot" - box plot without individual points and outliers, "barPlot" (default) - bar height represents the median signal value for a given cell type, "violinPlot" - violin plot with medians.
`cellGroup` | - This option allows to selcet a tissue type to be plotted, if NA (default) all available tissue types are ploted, available options: "blood", "bone", "CNS", "embryonic", "eye", "foreskin", "gastrointestinal", "heart", "liver", "lymphatic", "mammaryGland", "mouth", "respiratorySystem", "skeletalMuscle", "skin", "urinarySystem", "vasculature", can be passed as a character string or vector of strings.
`cellTypeMetadata` | Metadata for cell type - tissue association. This option is for users, who provide their own open region signal matrix. The cellTypeMetadata matrix must contain two columns called cellType and tissueType. cellType column containes the cell type names in the provided signalMatrix column names. The tissueType columns provides an information, which tissue the cell type comes from.
`colorScheme` | Provide color values for each tissueType if you want to change the default colors.

### Value

A ggplot object.

### Examples

    openRegionSummary = calcOpenSignal(vistaEnhancers, exampleOpenSignalMatrix_hg19)
    plotSignal = plotOpenSignal(openRegionSummary)
    plotSignal = plotOpenSignal(openRegionSummary, plotType = "jitter",
    cellGroup = "blood")

[Package GenomicDistributions version 1.2.0 Index]