plotProfiles: Plot functional profiles

In goProfiles: goProfiles: an R package for the statistical analysis of 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

aProf	Functional profile to plot
aTitle	Title for the figures
anOnto	Ontology (to appear in the title)
percentage	Plot absolute or relative frequencies (not summing to 100)
HORIZVERT	Plot horizontal or vertical bars
legendText	Text of the legend for the plot
colores	Colors to be used
multiplePlots	Plot all profiles for a given dataset in one figure
multipleWindows	Open a new window after each plot
labelWidth	Width of Y axis labels (Names of GO categories) in the plot
...	Other graphical parameters that should be passed for plotting

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)

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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 object is masked from 'package:base':

    expand.grid

Loading required package: GO.db

goProfiles documentation built on Nov. 8, 2020, 8:12 p.m.