Plot functional profiles

Description

Plots basic functional profiles created with the 'basicProfile' instruction. If several profiles have to be plot together they must be first merged using the 'mergeProfiles' function. The labels of the Y-axis of the plots are the descriptions of the GO Terms. If the label is longer than 20 characters it is truncated and ended by three dots.

Usage

plotProfiles(aProf, aTitle = "Functional Profile", anOnto = NULL, percentage = FALSE, 
HORIZVERT = TRUE, legendText = NULL, colores = c("white", "red"), multiplePlots = F, multipleWindows = T, labelWidth=25,...)

Arguments

Value

The plot

Author(s)

Alex Sanchez

Examples

require(goProfiles)
data(prostateIds)
welsh.MF <- basicProfile (welsh01EntrezIDs[1:100], onto="MF", level=2, orgPackage="org.Hs.eg.db") 
singh.MF <- basicProfile (singh01EntrezIDs[1:100], onto="MF", level=2, orgPackage="org.Hs.eg.db") 
plotProfiles(welsh.MF,'Functional profiles for Welsh dataset',percentage=TRUE)
welsh.singh.MF <-mergeProfilesLists(welsh.MF, singh.MF, profNames=c("Welsh", "Singh"))
plotProfiles(welsh.singh.MF , percentage=TRUE, multiplePlots=TRUE, labelWidth=30)

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)

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> library(goProfiles)
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: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GO.db

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/goProfiles/plotProfiles.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotProfiles
> ### Title: Plot functional profiles
> ### Aliases: plotProfiles
> ### Keywords: hplot
> 
> ### ** Examples
> 
> require(goProfiles)
> data(prostateIds)
> welsh.MF <- basicProfile (welsh01EntrezIDs[1:100], onto="MF", level=2, orgPackage="org.Hs.eg.db") 

> singh.MF <- basicProfile (singh01EntrezIDs[1:100], onto="MF", level=2, orgPackage="org.Hs.eg.db") 
> plotProfiles(welsh.MF,'Functional profiles for Welsh dataset',percentage=TRUE)
> welsh.singh.MF <-mergeProfilesLists(welsh.MF, singh.MF, profNames=c("Welsh", "Singh"))
> plotProfiles(welsh.singh.MF , percentage=TRUE, multiplePlots=TRUE, labelWidth=30)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>