R Under development (unstable) (2023-08-20 r84995 ucrt) -- "Unsuffered Consequences"
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> ###################################################
> ### chunk number 1: preliminaries
> ###################################################
> 
> library(classGraph)

Attaching package: 'classGraph'

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

    plot

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

    plot

> 
> stopifnot(require("Matrix"),
+           require("graph"))
Loading required package: Matrix
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

> 
> allCl <- getClasses("package:Matrix")
> ## Those called "...Matrix" :
> M.Cl <- grep("Matrix$",allCl, value = TRUE)
> 
> str(M3cl <- grep("^...Matrix$",M.Cl, value = TRUE))
 chr [1:48] "lgeMatrix" "dtrMatrix" "dgRMatrix" "lspMatrix" "lsTMatrix" ...
> 
> M3cl <- M3cl[M3cl != "corMatrix"] # corMatrix not desired in following
> 
> 
> 
> 
> 
> ###################################################
> ### chunk number 2: tree-Matrix
> ###################################################
> trMatrix <- classTree("Matrix") ; trMatrix
A graphNEL graph with directed edges
Number of Nodes = 74 
Number of Edges = 166 
> ## 2005-08: 58 nodes with 109 edges
> ## 2007-01: 74 nodes with 151 edges
> par(lwd = 0.3)# no effect --- learn to use Rgraphviz!!
> plotRag(mRagraph(trMatrix), subArgs=.optRagargs(adj = 0.5))
> 
> 
> ###################################################
> ### chunk number 3: sTree-M1
> ###################################################
> allN <- nodes(trMatrix)
> "%w/o%" <- function(x,y) x[!x %in% y] #--  x without y
> 
> hier1 <- paste(c("diagonal", "triangular", "symmetric", "general", "comp"),
+                "Matrix", sep = '') # composites can be factorized:  ^^^^
> 
> ## dropping 1st ``dim'' hierarchy -- much less edges:
> (trM1 <- subGraph(allN %w/o% hier1, trMatrix))
A graphNEL graph with directed edges
Number of Nodes = 69 
Number of Edges = 116 
> plotRag(mRagraph(trM1), subArgs=.optRagargs(adj = 0.5))
> 
> 
> ###################################################
> ### chunk number 4: sTree-top12
> ###################################################
> defMatrix <- getClassDef("Matrix")
> ## Distances of subclasses:
> table(subDist <- sapply(defMatrix@subclasses, slot, "distance"))

 1  2  3  4  5 
 9 18 44  3  2 
> sub12 <- defMatrix@subclasses[subDist <= 2] # but not unique!
> trM_top12 <- subGraph(c("Matrix", unique(names(sub12))), trMatrix)
> plotRag(mRagraph(trM_top12)) ## first and second level virtual classes
> 
> 
> ###################################################
> ### chunk number 5: sTree-sparse
> ###################################################
> trSpMatrix <- classTree("sparseMatrix")
> trSpMatrix
A graphNEL graph with directed edges
Number of Nodes = 39 
Number of Edges = 65 
> plotRag(mRagraph(trSpMatrix, "dot"),
+         subArgs= .optRagargs(side = 3, adj = 1, line = 0),
+         main = "'sparseMatrix' classes -- sub graph")
> 
> 
> ###################################################
> ### chunk number 6: sTree-sp-neato
> ###################################################
> ## now this *does* look kind of neat:
> plotRag(mRagraph(trSpMatrix, "neato"),
+         subArgs= .optRagargs(side = 3, adj = 1, line = 0),
+         main = "'sparseMatrix' classes -- in \"neato\" layout")
Warning messages:
1: In arrows(head_from[1], head_from[2], head_to[1], head_to[2], col = edgeColor,  :
  zero-length arrow is of indeterminate angle and so skipped
2: In arrows(head_from[1], head_from[2], head_to[1], head_to[2], col = edgeColor,  :
  zero-length arrow is of indeterminate angle and so skipped
3: In arrows(head_from[1], head_from[2], head_to[1], head_to[2], col = edgeColor,  :
  zero-length arrow is of indeterminate angle and so skipped
> ## all three others do not
> 
> 
> 
> proc.time()
   user  system elapsed 
   2.54    0.29    2.89