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Last data update: 2014.03.03

R: function to visualize interactions as a levelplot

InteractLevelPlot

R Documentation

function to visualize interactions as a levelplot

Description

visualizes significant interactions as a levelplot

Usage

InteractLevelPlot(toptable, thresh = 0.001, by = "P.Value", key = FALSE, col.regions = colorRampPalette(c("blue", "white", "yellow")),zerolimit=0)

Arguments

`toptable`	`toptable` table from function topTable
`thresh`	`thresh` numeric, threshold for significance
`by`	`by` column in topTable that thresh should be applied to
`key`	`key` optional, data frame with groupings of the genes in the toptable
`col.regions`	`col.regions` colors to be used
`zerolimit`	`zerolimit` threshold below which interactions should be colored as 0.

Value

a levelplot, pdf files with graphs

Author(s)

Elin Axelsson

Examples


data(screen1_raw)
df = cellHTS2df(screen1_raw,neutral="Fluc")
tt = data.frame("size"=runif(length(unique(df$Pair[df$Type=="comb"])),-2,2),stringsAsFactors=FALSE)
rownames(tt) = unique(df$Pair[df$Type=="comb"])
InteractLevelPlot(tt,thres=0,by="size")

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(coRNAi)
Loading required package: cellHTS2
Loading required package: RColorBrewer
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")'.

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: grid
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/coRNAi/InteractLevelPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: InteractLevelPlot
> ### Title: function to visualize interactions as a levelplot
> ### Aliases: InteractLevelPlot
> 
> ### ** Examples
> 
> 
> data(screen1_raw)
> df = cellHTS2df(screen1_raw,neutral="Fluc")
> tt = data.frame("size"=runif(length(unique(df$Pair[df$Type=="comb"])),-2,2),stringsAsFactors=FALSE)
> rownames(tt) = unique(df$Pair[df$Type=="comb"])
> InteractLevelPlot(tt,thres=0,by="size")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>