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Last data update: 2014.03.03

R: Double Perturbation Plot

plotDoublePerturbation

R Documentation

Double Perturbation Plot

Description

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.

Usage

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, ...)

Arguments

`sgi`	An object of class `RNAinteract`.
`target`	A character name of the target gene.
`screen`	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.
`channel`	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.
`withoutgroups`	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.
`design`	The Either `"template"` (default) or `"query"`. The single perturbation effects are either the template main effects or the query main effects.
`main`	An overall title of the plot.
`xlab`	A title of the x-axis.
`ylab`	A title of the y-axis.
`range`	A numeric vector of length two. range equals the `xlim`, `ylim` argument in plot.
`show.labels`	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.
`label.par`	Cut-off value for q.value or p.value for displaying text labels (See `show.labels`).
`label`	Either a character vector with gene names, or a named vector of text labels. The names of the vector represent the gene names.
`avoid.overlap`	If `TRUE` (default), text is moved such that text labels are not overlapping.
`col`	A named vector with colors. The names of `col` define which points are colored (See also `fill`).
`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.
`D,MT,MQ,PV,QV,PI`	Internal usage.
`...`	Further argument passed to `grid.doublePerturbation` or `doublePerturbationGrob`.

Details

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

Value

A grob is returned.

Author(s)

Bernd Fischer

Examples

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

Results


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,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 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")
doublePerturbation[GRID.doublePerturbation.11] 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>