Double Perturbation Plot Grob

Description

These functions create a double perturbation grob for interaction screens. All interactions of one gene are displayed in one panel. The double perturbation readout level is plotted against the single perturbation level.

Usage

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doublePerturbationGrob( mainEffect, dpEffect, mainEffectTarget,
                       range=NULL, main=NULL, xlab=NULL, ylab=NULL,
                       text=NULL, avoid.overlap=TRUE,
                       axisOnOrigin = FALSE,
                       drawBox = TRUE,
		       pch = 21, size=unit(1, "char"), fill = NULL,
                       gpMain = gpar(lty="dashed", lwd=3, col="cyan"),
                       gpNI = gpar(lty="dashed", lwd=3, col="orange"),
                       gpPoints = gpar(pch=21),
                       gpText = NULL,
                       gpAxis = NULL,
                       gpWTLines=NULL,
                       name=NULL, gp=NULL, vp=NULL )
grid.doublePerturbation(..., draw = TRUE)

# a helper function for doublePerturbationGrob:
postDrawDetails.doublePerturbation(x, recording)

Arguments

mainEffect

A numeric vector of main effects.

dpEffect

A numeric vector of double perturbation effects.

mainEffectTarget

The main effect of the target gene (A single numeric value).

range

The range of the plot. Equals the xlim, ylim arguments of plot.

main

An overall title of the plot.

xlab

A title of the x-axis.

ylab

A title of the y-axis.

text

A character vector of text. Has to have the same length as mainEffect.

avoid.overlap

If TRUE (default) the text labels are moved such that the text is not overlapping.

axisOnOrigin

If TRUE, the x- and y-axis are draw on the origin of the data. If FALSE (default), the axis are drawn on the left and on the bottom.

drawBox

If TRUE (default), a box is drawn around the plot.

pch

Either an integer specifying a symbol or a single character to be used in plotting points. See points for possible values.

size

A unit object specifying the size of the plotting symbols.

fill

A list containing (some of) the following elements: col defines a fill color for the points. Either a single value or a vector of the same length as mainEffect. If col is defined, all other elements of fill have no effect. values is a numeric vector of the same length as mainEffcet that contains values that are mapped to colors. at is a numeric vector indicating breakpoints along the values. If not specified will be equally spaced on the range of the values. colors defines a set of colors from which a colorramp is created. colramp defines a colorramp directly. colramp has no effect, if colors is defined.

gp

An object of class gpar, typically the output from a call to the function gpar. This is basically a list of graphical parameter settings. Overall settings for the plot are set in gp.

gpMain,gpNI

An object of class gpar (See gp). gpMain and gpNI indicate the graphics parameter for the main effect lines and the non-interacting line.

gpPoints,gpText,gpAxis,gpWTLines

An object of class gpar (See gp). These arguments define graphical parameters for single compartments of the plot.

name

A character identifier.

vp

A Grid viewport object (or NULL).

draw

If TRUE the grob is drawn on the current device.

...

Further arguments passed to doublePerturbationGrob.

x, recording

Internal usage only.

Details

This function creates a grob for a double perturbation plot. It is probably more convenient to use the function plotDoublePerturbation.

Value

A grob is returned.

Author(s)

Bernd Fischer

See Also

RNAinteract-package, plotDoublePerturbation, reportDoublePerturbation

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