README.Rmd

---
output: md_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 8,
  fig.height = 6,
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# snifter
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R binding for [openTSNE](https://opentsne.readthedocs.io/en/latest/index.html)
using [basilisk](https://bioconductor.org/packages/devel/bioc/html/basilisk.html).

## Example usage

Basic usage of the function returns a matrix of t-SNE coordinates.

```{r}
library("snifter")
set.seed(42)
m <- matrix(rnorm(20000), ncol = 20) 
snifter <- fitsne(m[-(1:2), ], random_state = 42L)
plot(snifter, pch = 19, xlab = "t-SNE 1", ylab = "t-SNE 2")
```

We can also project new points into an existing embedding.

```{r}
n <- 20
snifter <- fitsne(m[-(1:n), ], random_state = 42L)
plot(snifter, pch = 19, col = "black",
    xlab = "t-SNE 1", ylab = "t-SNE 2")
new <- project(snifter, m[1:n, ], old = m[-c(1:n), ])
points(new, pch = 19, col = "red")
```