R Under development (unstable) (2024-10-21 r87258 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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("Mercator")
Loading required package: Thresher
Loading required package: ClassDiscovery
Loading required package: cluster
Loading required package: oompaBase
Loading required package: PCDimension
> 
> ## test names part
> set.seed(853845)
> X <- matrix(sample(c(0,1), 10*30, replace=TRUE), 10, 30)
> B <- BinaryMatrix(X)
> 
> J <- Mercator(B, "jaccard", "mds", 3)
> J <- addVisualization(J, "tsne", perplexity=5)
> J <- addVisualization(J, "graph")
> G <- J@view[["graph"]]
> ## There used to be a bug that caused thie next line to fail when row names
> ## or column names were NULL. If this works, then we haven't broken it again.
> plot(G$graph, layout=G$layouts[["nicely"]])
> plot(J, view = "graph", layout = "nicely")
> ## There is an issue in igraph if nodes are placed at (nearly?) identical
> ## locations. This was fixed inside the 'plot' method  by 'jittering" the
> ## locations.
> plot(J, view = "graph", layout = "mds")
> plot(J, view = "graph", layout = "tsne")
> 
> ## Need to see if we still assume that visualizations exist
> J <- Mercator(B, "jaccard", "hclust", 3)
> J <- addVisualization(J, "graph")
> G <- J@view[["graph"]]
> names(G$layouts)
[1] "nicely"
> 
> 
> proc.time()
   user  system elapsed 
   2.39    0.31    2.70