Last data update: 2014.03.03

R: Double Perturbation Plot
plotDoublePerturbationR Documentation

Double Perturbation Plot


These function draws a double perturbation plot 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.


plotDoublePerturbation( sgi, screen, channel, target,
                       withoutgroups = c("neg", "pos"), design,
                       main, xlab, ylab, range,
                       show.labels = "none", label.par, label,
		       avoid.overlap, col, fill,
                       D , MT, MQ, PV, QV, PI, ...)



An object of class RNAinteract.


A character name of the target gene.


The character name of the screen to display. If not specified, the first screen is used. Does not have to be specified, if sgi contains only one screen.


The character name of the channel to display. If not specified, the first channel is used. Does not have to be specified, if sgi contains only one channel.


Interactions to genes from these groups (as specified in the reagent or target annotation) are excluded from the plot, e.g. positive and negative controls.


The Either "template" (default) or "query". The single perturbation effects are either the template main effects or the query main effects.


An overall title of the plot.


A title of the x-axis.


A title of the y-axis.


A numeric vector of length two. range equals the xlim, ylim argument in plot.


Automatically select text labels for the points. 'all' shows a text label for all genes, "q.value" and "p.value" show a text label for all genes with a q.value (p.value) larger than label.par, "none" does not show any text label. This argument has no effect, if label is specified.


Cut-off value for q.value or p.value for displaying text labels (See show.labels).


Either a character vector with gene names, or a named vector of text labels. The names of the vector represent the gene names.


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


A named vector with colors. The names of col define which points are colored (See also fill).


A list up to four values. colors defines a set of colors from which a colorramp is created. If colramp is specified, colors has no effect. colramp directly specifies the colorramp. values define the values that are color coded. If values is not specified, the pairwise interaction term is used instead. at is a numeric vector defining the breakpoints along the values. If not specified, breakpoints are selected to range three times the standard deviation of the values around zero. fill has no effect, if col is specified.


Internal usage.


Further argument passed to grid.doublePerturbation or doublePerturbationGrob.


Plots a double perturbation plot. It shows the interaction profile for one (query) gene.


A grob is returned.


Bernd Fischer

See Also

RNAinteract-package, grid.doublePerturbation, reportDoublePerturbation


plotDoublePerturbation( sgi, screen="1", channel="nrCells", target="rl", show.labels="p.value")


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RNAinteract)
Loading required package: abind
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,, cbind, colnames,, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax,, pmin,, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAinteract/plotDoublePerturbation.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotDoublePerturbation
> ### Title: Double Perturbation Plot
> ### Aliases: plotDoublePerturbation
> ### Keywords: hplot
> ### ** Examples
> data("sgi")
> plotDoublePerturbation( sgi, screen="1", channel="nrCells", target="rl", show.labels="p.value")
null device