As the title says it should do something with class relationships

buildClassDepGraph(class, includeUnions = FALSE)

buildClassDepData(class, includeUnions = FALSE)

buildClassDepFromPackage(pkg, includeUnions = FALSE)

plotClassDep(class, includeUnions = FALSE)

plotClassDepData(data)

plotClassDepGraph(g)

Arguments

class

a single character value defining a ‘S4’ class name

includeUnions

TRUE or FALSE: Should union definitions included in the result? (default: FALSE)

pkg

a single character value defining a package name

data

a data.frame with compatible columns. See output of buildClassDepData

g

an igraph object with compatible edge attributes. See output of buildClassDepGraph

Examples

library("SummarizedExperiment")
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: ‘matrixStats’
#> The following object is masked from ‘package:dplyr’:
#> 
#>     count
#> 
#> Attaching package: ‘MatrixGenerics’
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: generics
#> 
#> Attaching package: ‘generics’
#> The following objects are masked from ‘package:igraph’:
#> 
#>     components, union
#> The following object is masked from ‘package:dplyr’:
#> 
#>     explain
#> The following objects are masked from ‘package:base’:
#> 
#>     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#>     setequal, union
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:igraph’:
#> 
#>     normalize, path
#> The following object is masked from ‘package:dplyr’:
#> 
#>     combine
#> 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, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#>     unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: ‘S4Vectors’
#> The following objects are masked from ‘package:dplyr’:
#> 
#>     first, rename
#> The following object is masked from ‘package:utils’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> 
#> Attaching package: ‘IRanges’
#> The following objects are masked from ‘package:dplyr’:
#> 
#>     collapse, desc, slice
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: ‘Biobase’
#> The following object is masked from ‘package:MatrixGenerics’:
#> 
#>     rowMedians
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     anyMissing, rowMedians
#> Warning: replacing previous import ‘S4Arrays::makeNindexFromArrayViewport’ by ‘DelayedArray::makeNindexFromArrayViewport’ when loading ‘SummarizedExperiment’
depData <- buildClassDepData("RangedSummarizedExperiment")
depData
#>                        parent                child   type parentVirtual
#> 1  RangedSummarizedExperiment SummarizedExperiment object         FALSE
#> 2        SummarizedExperiment      RectangularData object         FALSE
#> 3        SummarizedExperiment               Vector object         FALSE
#> 5                      Vector            Annotated object          TRUE
#> 7  RangedSummarizedExperiment            DataFrame   slot         FALSE
#> 8  RangedSummarizedExperiment                 list   slot         FALSE
#> 9  RangedSummarizedExperiment        GenomicRanges   slot         FALSE
#> 10 RangedSummarizedExperiment          GRangesList   slot         FALSE
#> 11 RangedSummarizedExperiment               Assays   slot         FALSE
#> 12 RangedSummarizedExperiment            character   slot         FALSE
#> 13                  DataFrame      RectangularData   slot          TRUE
#> 14                  DataFrame                 List   slot          TRUE
#> 16                       List               Vector   slot          TRUE
#> 18                     Vector            Annotated   slot          TRUE
#> 20                  DataFrame      RectangularData   slot          TRUE
#> 21                  DataFrame                 List   slot          TRUE
#> 23                       List               Vector   slot          TRUE
#> 25                     Vector            Annotated   slot          TRUE
#> 27                       list               vector   slot         FALSE
#> 33              GenomicRanges               Ranges   slot          TRUE
#> 37                     Ranges                 List   slot          TRUE
#> 38                       List               Vector   slot          TRUE
#> 40                     Vector            Annotated   slot          TRUE
#> 42                GRangesList    GenomicRangesList   slot          TRUE
#> 44          GenomicRangesList           RangesList   slot          TRUE
#> 46                 RangesList                 List   slot          TRUE
#> 47                       List               Vector   slot          TRUE
#> 49                     Vector            Annotated   slot          TRUE
#> 51                     Assays      RectangularData   slot          TRUE
#> 53                  character               vector   slot         FALSE
#>    parentUnion childVirtual childUnion
#> 1        FALSE        FALSE      FALSE
#> 2        FALSE         TRUE      FALSE
#> 3        FALSE         TRUE      FALSE
#> 5        FALSE         TRUE      FALSE
#> 7        FALSE         TRUE      FALSE
#> 8        FALSE        FALSE      FALSE
#> 9        FALSE         TRUE      FALSE
#> 10       FALSE         TRUE      FALSE
#> 11       FALSE         TRUE      FALSE
#> 12       FALSE        FALSE      FALSE
#> 13       FALSE         TRUE      FALSE
#> 14       FALSE         TRUE      FALSE
#> 16       FALSE         TRUE      FALSE
#> 18       FALSE         TRUE      FALSE
#> 20       FALSE         TRUE      FALSE
#> 21       FALSE         TRUE      FALSE
#> 23       FALSE         TRUE      FALSE
#> 25       FALSE         TRUE      FALSE
#> 27       FALSE         TRUE      FALSE
#> 33       FALSE         TRUE      FALSE
#> 37       FALSE         TRUE      FALSE
#> 38       FALSE         TRUE      FALSE
#> 40       FALSE         TRUE      FALSE
#> 42       FALSE         TRUE      FALSE
#> 44       FALSE         TRUE      FALSE
#> 46       FALSE         TRUE      FALSE
#> 47       FALSE         TRUE      FALSE
#> 49       FALSE         TRUE      FALSE
#> 51       FALSE         TRUE      FALSE
#> 53       FALSE         TRUE      FALSE
g <- buildClassDepGraph("RangedSummarizedExperiment")
plotClassDepGraph(g)