TSSi (version 1.18.0)

plot-methods: Plot methods

Description

Plot the data and results of the TSSi package.

Usage

plot(x, y, ...)

Arguments

x

An object of class TssData, TssNorm, or TssResult.

y

A single integer or character string specifying which segment to plot. An integer is interpreted as the index of the segment while a character string is matched against the segment names.

...

Optional arguments used in order to customize the figure. See the ‘details’ section.

Methods

Visualize the raw data:

plot:

signature(x="TssData")

plot(x, y, counts=TRUE, legend=TRUE, ...)

Visualize the normalized data:

plot:

signature(x="TssNorm")

plot(x, y, counts=TRUE, ratio=TRUE, fit=TRUE, legend=TRUE, ...)

Visualize the normalized data along with the identified TSS:

plot:

signature(x="TssResult")

plot(x, y, counts=TRUE, ratio=TRUE, fit=TRUE, expect=FALSE, tss=TRUE, threshold=TRUE, rug=TRUE, legend=TRUE, ...)

Details

With the plot method, the raw, normalized, or final data can easily be visualized.

The plot method uses a special system in order to customize the graphical elements of the figure. It allows to refer to the different components with the name of the additional input argument; its value is a list containing named graphical parameters for the underlying plot function. The following list describes the available names and their contribution.

plot

Graphical parameters for the axes and the labeling, passed to the plot function.

counts

Logical indicating whether the raw counts should be plotted.

countsArgs

Graphical parameters for the ‘counts’ variable, passed to the points function.

ratio

Logical indicating whether the estimates based on the Poisson ratios should be plotted.

ratioArgs

Graphical parameters for the ‘ratio’ variable, passed to the points function.

fit

Logical indicating whether the estimates based on the fitting should be plotted.

fitArgs

Graphical parameters for the ‘fit’ variable, passed to the points function.

expect

Logical indicating whether the background estimates should be plotted.

expectArgs

Graphical parameters for the ‘expect’ variable, passed to the points function.

expect

Logical indicating whether the background estimates should be computed for all positions, rather than only for those with reads.

tss

Logical indicating whether the identified TSS should be plotted.

tssArgs

Graphical parameters for the ‘tss’ variable, passed to the points function.

threshold

Logical indicating whether the threshold parameter used in the identification step should be indicated.

thresholdArgs

Graphical parameters for the ‘threshold’ variable, passed to the abline function.

rug

Logical indicating whether the location of the identified TSS should be indicated.

rugArgs

Graphical parameters for the ‘rug’ variable, passed to the rug function.

baseline

Logical indicating whether a baseline indicating zero reads should be drawn.

baselineArgs

Graphical parameters for the ‘baseline’ variable, passed to the abline function.

legend

Logical indicating whether a legend should be plotted.

legendArgs

Graphical parameters for the ‘legend’ variable, passed to the legend function.

Thus, for (a) omitting the ratio estimates, the threshold, and the legend, (b) customizing the graphical parameters of the raw read counts, (c) customizing the axis labels and the title, the following code can be used: plot(x, 1, ratio=FALSE, threshold=FALSE, legend=FALSE, countsArgs=list(type="h", col="darkgray", pch=NA), plotArgs=list(xlab="Genomic position", main="TSS for segment 's1_-_155'")

See Also

Classes: TssData, TssNorm, TssResult Methods: segmentizeCounts, normalizeCounts, identifyStartSites, get-methods, plot-methods, asRangedData-methods

Functions: subtract-functions

Data set: physcoCounts

Package: TSSi-package

Examples

## preceding steps
example(identifyStartSites)

## plot
plot(yFit, 1)

## plot w/ some custom settings
plot(z, 1, ratio=FALSE, threshold=FALSE, countsArgs=list(type="h",
col="darkgray", pch=NA), plotArgs=list(xlab="Genomic position",
main="TSS for segment 's1_-_155'"))