Description Usage Arguments Value References Examples

Plot principle components of the proximity matrix

1 2 3 |

`pca` |
a prcomp object, pca of an n x n matrix giving the proportion of times across all trees that observation i,j are in the same terminal node |

`dims` |
integer vector of length 2 giving indices for the dimensions of |

`labels` |
length n character vector giving observation labels |

`alpha` |
optional continuous vector of length n make points/labels transparent or a numeric of length 1 giving the alpha of all points/labels |

`alpha_label` |
character legend title if alpha parameter used |

`color` |
optional discrete vector of length n which colors the points/labels or a character vector giving the color of all points/labels |

`color_label` |
character legend title if color parameter is used |

`shape` |
optional discrete vector of length n which shapes points (not applicable if labels used) or a character vector of length 1 which gives the shape of all points |

`shape_label` |
character legend title if shape parameter is used |

`size` |
optional continuous vector of length n which sizes points or labels or a numeric of length 1 which gives the sizes of all the points |

`size_label` |
character legend title if size parameter used |

`xlab` |
character x-axis label |

`ylab` |
character y-axis label |

`title` |
character plot title |

a ggplot object

https://github.com/vqv/ggbiplot

Gabriel, "The biplot graphic display of matrices with application to principal component analysis," *Biometrika*, 1971

1 2 3 4 5 6 7 8 9 10 11 | ```
library(randomForest)
fit = randomForest(hp ~ ., mtcars, proximity = TRUE)
prox = extract_proximity(fit)
pca = prcomp(prox, scale = TRUE)
plot_prox(pca, labels = row.names(mtcars))
fit = randomForest(Species ~ ., iris, proximity = TRUE)
prox = extract_proximity(fit)
pca = prcomp(prox, scale = TRUE)
plot_prox(pca, color = iris$Species, color_label = "Species", size = 2)
``` |

```
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
```

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