boxplotSpike: plot boxplots of ChIP-seq experiments

In descostesn/ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

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)

descostesn/ChIPSeqSpike documentation built on Aug. 6, 2019, 3:51 p.m.