R Under development (unstable) (2024-06-20 r86796 ucrt) -- "Unsuffered Consequences"
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> library(RPointCloud)
> data(CLL)
> view <- cmdscale(daisydist)
> circular <- angleMeans(view, ripdiag, NULL, clinical)
> lf <- LoopFeature(circular)
> round(sort(lf@Kstat), 4)
                    CatB2M                  Rai.Stage 
                    0.1140                     0.1264 
                    CatRAI                     LogB2M 
                    0.1265                     0.1347 
Serum.beta.2.microglobulin                 Hemoglobin 
                    0.1502                     0.2553 
       Light.chain.subtype            mutation.status 
                    0.2990                     0.3153 
                    LogLDH                     stat11 
                    0.3335                     0.3404 
     Hypogammaglobulinemia                     Dohner 
                    0.3603                     0.3658 
              Zap70Protein                  Serum.LDH 
                    0.3945                     0.4135 
                   CatCD38                     Purity 
                    0.4305                     0.4546 
                    stat13          White.blood.count 
                    0.5932                     0.7432 
                    CatWBC                     stat17 
                    0.7618                     0.7661 
                 Platelets                        Sex 
                    0.7721                     0.7828 
      Massive.Splenomegaly             Prolymphocytes 
                    0.7931                     0.8035 
                   AgeAtDx                     stat12 
                    0.8472                     0.8696 
                    LogWBC                       Race 
                    0.8774                     0.9089 
                   Matutes 
                    0.9184 
> opar <- par(mai = c(0.82, 0.2, 0.82, 1.82))
> image(lf, main = "Clinical Factors in CLL")
> par(opar)
> 
> plot(lf, "mutation.status")
> opar <- par(mfcol = c(2,2))
> plot(lf, c("Serum.beta.2.microglobulin", "Hemoglobin",
+            "Rai.Stage", "LogLDH"))
> par(opar)
> 
> 
> proc.time()
   user  system elapsed 
   2.57    0.39    2.96