Simple UMAP example with parameters in R

umap_example.Rmd

---
title: "umap_example"
output: html_document
---

```{r setup}
library(uwot)
library(ggplot2)
```

```{r message=FALSE, warning=FALSE}
data(iris)

iris_features <- iris[, 1:4]
iris_labels <- iris$Species

umap_embeddings <- umap(iris_features, n_neighbors = 15, n_components = 2, 
                        min_dist = 0.5, metric = "euclidean")
                    
df <- data.frame(UMAP1 = umap_embeddings[,1],
                 UMAP2 = umap_embeddings[,2],
                 Species = iris_labels)
                 
 ggplot(df, aes(x = UMAP1, y = UMAP2, color = Species)) +
  geom_point(size = 3, alpha = 0.8) +
  ggtitle("UMAP of the Iris data set") +
  theme_bw()
```