README.Rmd

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# liminal

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**liminal** is an R package for constructing interactive visualisations designed
for exploratory high-dimensional data analysis. It's main purpose is to
combine tours with (non-linear) dimension reduction algorithms to provide a
more holistic view of the geometry and topology of a dataset. These
are designed for data analysts first, so they render either inside the
RStudio Viewer pane or from a web-browser using **shiny**.

There are two main functions for generating tour interfaces:
  
* The basic tour animation via `limn_tour()`
* Linking tours to another view `limn_tour_link()`

The goal of **liminal** is to provide complementary visualisations for use with
understanding embedding algorithms such as tSNE.  It has been
[shown](https://distill.pub/2016/misread-tsne/) that in order to produce an
'effective' embedding one may have to play with hyperparamters and various
settings for these algorithms. **liminal** allows you to see how different
parameterisations warps the underlying high-dimensional space.

See the [liminal vignette](https://sa-lee.github.io/liminal/articles/liminal.html) for details of package usage
and our [arXiv preprint](https://arxiv.org/abs/2012.06077) for a complete discussion on how to apply **liminal** to real data analysis workflows like clustering.

## Quick Start

The release version of **liminal** is available on CRAN:

```{r, eval = FALSE}
install.packages("liminal")
```

The development version of **liminal** can be installed as follows:

```{r, eval = FALSE}
# install.packages("remotes")
remotes::install_github("sa-lee/liminal")
```

You can generate a tour view that will load in the Rstudio Viewer pane:

```{r, eval = FALSE}
library(liminal)
limn_tour(fake_trees, dim1:dim10)
```

The interface provides instructions on how to use it, click on the help button
to get started!