boxplotSpike: plot boxplots of ChIP-seq experiments

Description Usage Arguments Details Value Methods (by class) Author(s) See Also Examples

Description

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

Usage

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  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)

Author(s)

Nicolas Descostes

See Also

spikeDataset spikePipe plotProfile plotTransform plotHeatmaps plotCor

Examples

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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)

ChIPSeqSpike documentation built on Nov. 8, 2020, 5:29 p.m.