boxplotSpike {ChIPSeqSpike} | R Documentation

## plot boxplots of ChIP-seq experiments

### Description

plot boxplots of the mean values of ChIP-seq experiments on the annotations given to the extractBinding method

### Usage

      boxplotSpike(theObject, col = NULL, rawFile = FALSE,
                    rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE,
                    spiked = TRUE, ylab = NULL, outline = TRUE, violinPlot = FALSE,
                    notch = TRUE, mean_with_sd = FALSE, mean = FALSE,
                    median = FALSE, boxplot = FALSE, jitter = FALSE, plot = TRUE,
                    verbose = FALSE)

    ## S4 method for signature 'ChIPSeqSpikeDataset'
    boxplotSpike(theObject, col = NULL, rawFile =
    FALSE, rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE, spiked = TRUE, ylab
    = NULL, outline = TRUE, violinPlot = FALSE, notch = TRUE, mean_with_sd = FALSE,
     mean = FALSE, median = FALSE, boxplot = FALSE, jitter = FALSE, plot = TRUE,
    verbose = FALSE)

    ## S4 method for signature 'ChIPSeqSpikeDatasetBoost'
    boxplotSpike(theObject, col = NULL,
    rawFile = FALSE, rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE,
    spiked = TRUE, ylab = NULL, outline = TRUE, violinPlot = FALSE, notch = TRUE,
    mean_with_sd = FALSE, mean = FALSE, median = FALSE, boxplot = FALSE,
    jitter = FALSE, plot = TRUE, verbose = FALSE)

    ## S4 method for signature 'ChIPSeqSpikeDatasetList'
    boxplotSpike(theObject, col = NULL, rawFile
    = FALSE, rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE, spiked = TRUE,
    ylab = NULL, outline = TRUE, violinPlot = FALSE, notch = TRUE, mean_with_sd =
    FALSE, mean = FALSE, median = FALSE, boxplot = FALSE, jitter = FALSE,
    plot = TRUE, verbose = FALSE)

    ## S4 method for signature 'ChIPSeqSpikeDatasetListBoost'
    boxplotSpike(theObject, col = NULL,
    rawFile = FALSE, rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE,
    spiked = TRUE, ylab = NULL, outline = TRUE, violinPlot = FALSE, notch = TRUE,
    mean_with_sd = FALSE, mean = FALSE, median = FALSE, boxplot = FALSE,
    jitter = FALSE, plot = TRUE, verbose = FALSE)

### Arguments

`theObject` | `ChIPSeqSpike` dataset (see ?spikeDataset)
`col` | Vector of colors for each experiment. Default is NULL.
`rawFile` | If TRUE, use the untransformed data. Not available in boost mode. Default is FALSE. (see details)
`rpmFile` | If TRUE, use the RPM scaled data. Not available in boost mode. Default is FALSE. (see details)
`bgsubFile` | If TRUE, use the input subtracted data. Not available in boost mode. Default is FALSE. (see details)
`revFile` | If TRUE, use the RPM reverted data. Not available in boost mode. Default is FALSE. (see details)
`spiked` | If TRUE, use the spiked data. Default is TRUE. (see details)
`ylab` | Character string of the name of the y-axis. Default is NULL.
`outline` | Logical indicating if outliers are shown. Default is TRUE.
`violinPlot` | Logical indicating if a violin plot representation is used. Default is FALSE.
`notch` | Logical indicating if confidence intervals are shown. Default is TRUE.
`mean_with_sd` | Logical indicating if the mean and standard deviation are shown on the violin plot. Default is FALSE.
`mean` | Logical indicating if the mean is shown on the violin plot. Default is FALSE.
`median` | Logical indicating if the median is shown on the violin plot. Default is FALSE.
`boxplot` | Logical indicating if boxplot is shown on the violin plot. Default is FALSE
`jitter` | Logical indicating if each mean values is represented as a point on the violin plot. Default is FALSE.
`plot` | Logical indicating if the boxplot should be plotted. Default is TRUE.
`verbose` | Logical indicating if processing messages are shown. Default is FALSE.

### Details

The 'rawFile', 'rpmFile', 'bgsubFile', 'revFile', 'spiked' parameters indicate if the untransformed, RPM scaled, input DNA subtracted, RPM reversed or spiked data should be plotted. This option is only available if not in boost mode (see ?spikePipe for details on what these steps are).

### Value

Return a list with the components 'stats', 'n', 'conf', 'out', 'group' and 'names'. See ?boxplot for details.

### Methods (by class)

- `ChIPSeqSpikeDataset`: Method for signature theObject= 'ChIPSeqSpikeDataset'

- `ChIPSeqSpikeDatasetBoost`: Method for signature theObject= 'ChIPSeqSpikeDatasetBoost'

- `ChIPSeqSpikeDatasetList`: Method for signature theObject= 'ChIPSeqSpikeDatasetList'

- `ChIPSeqSpikeDatasetListBoost`: Method for signature theObject= 'ChIPSeqSpikeDatasetListBoost'

### Author(s)

Nicolas Descostes

### See Also

`spikeDataset` `spikePipe` `plotProfile` `plotTransform` `plotHeatmaps` `plotCor`

### Examples

    data("result_extractBinding")
    boxplotSpike(csds)
    boxplotSpike(csds, outline = FALSE, violinPlot = TRUE)
    boxplotSpike(csds, outline = FALSE, violinPlot = TRUE, mean = TRUE, jitter =
    TRUE)
    boxplotSpike(csds, rawFile = TRUE, rpmFile = TRUE, bgsubFile = TRUE, revFile =
    TRUE, spiked = TRUE, outline = FALSE, violinPlot = TRUE)

[Package ChIPSeqSpike version 1.6.0 Index]