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
> data("CML500")
> 
> ## Jaccard
> vis1 <- Mercator(CML500, "jacc", "mds", K=20)
> head(Mercator:::symv(vis1)) # make sure names propagate correctly
 S3.2.0  S4.1.0 S35.1.0 S49.1.0 S57.1.0 S59.1.0 
     16      16      16      16      16      16 
> head(Mercator:::colv(vis1))
   S3.2.0    S4.1.0   S35.1.0   S49.1.0   S57.1.0   S59.1.0 
"#2E91E5" "#E15F99" "#1CA71C" "#FB0D0D" "#E15F99" "#E15F99" 
> head(vis1@clusters)
 S3.2.0  S4.1.0 S35.1.0 S49.1.0 S57.1.0 S59.1.0 
      1       2       3       4       2       2 
> plot(vis1, main = "MDS") # default MDS view
> 
> barplot(vis1)
> scatter(vis1, view = "mds", main = "MDS")
> 
> ## t-SNE
> vis1 <- addVisualization(vis1, "tsne", perplexity=30)
> plot(vis1, view = "tsne", main = "t-SNE")
> 
> scatter(vis1, view = "tsne", colramp = grDevices::terrain.colors, main = "t-SNE")
> 
> ## hclust
> vis1 <- addVisualization(vis1, "hclust")
> plot(vis1, view = "hclust")
> 
> ## now test the igraph part
> vis1 <- addVisualization(vis1, "graph")
> plot(vis1, view = "graph") # default layout
> plot(vis1, view = "graph", layout = "nicely") # default layout
> plot(vis1, view = "graph", layout = "mds")
> plot(vis1, view = "graph", layout = "tsne")
> 
> ## umap
> vis1 <- addVisualization(vis1, "umap")
> plot(vis1, view = "umap", main="UMAP")
> 
> scatter(vis1, view = "umap", main="UMAP")
> 
> ## som
> vis1 <- addVisualization(vis1, "som")
> plot(vis1, view = "som")
> plot(vis1, view = "som", type = "counts")
> plot(vis1, view="som", type = "dist.neighbours", palette.name = topo.colors)
> 
> proc.time()
   user  system elapsed 
  17.18   10.59   27.76