https://github.com/sa-lee/liminal
Multivariate Visualisations with Tours and Embeddings
https://github.com/sa-lee/liminal
embedding-algorithms interactive-visualizations r-package t-sne tour
Last synced: 2 months ago
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Multivariate Visualisations with Tours and Embeddings
- Host: GitHub
- URL: https://github.com/sa-lee/liminal
- Owner: sa-lee
- License: other
- Created: 2019-10-09T03:11:16.000Z (about 6 years ago)
- Default Branch: main
- Last Pushed: 2021-05-28T08:52:07.000Z (over 4 years ago)
- Last Synced: 2025-06-12T15:04:27.932Z (4 months ago)
- Topics: embedding-algorithms, interactive-visualizations, r-package, t-sne, tour
- Language: R
- Homepage: https://sa-lee.github.io/liminal
- Size: 6.64 MB
- Stars: 5
- Watchers: 3
- Forks: 1
- Open Issues: 3
-
Metadata Files:
- Readme: README.Rmd
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
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README
---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
# liminal
[](https://github.com/sa-lee/liminal/actions)
[](https://CRAN.R-project.org/package=liminal)
**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!