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https://github.com/bodenmillergroup/sp2rd

R package to generate animated transitions between spatial locations and reduced dimensional embeddings

https://github.com/bodenmillergroup/sp2rd

Science Score: 23.0%

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Last synced: 10 months ago · JSON representation

Repository

R package to generate animated transitions between spatial locations and reduced dimensional embeddings

Basic Info
  • Host: GitHub
  • Owner: BodenmillerGroup
  • License: mit
  • Language: R
  • Default Branch: main
  • Size: 2.88 MB
Statistics
  • Stars: 0
  • Watchers: 5
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 3 years ago · Last pushed over 3 years ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  gganimate = list(
    nframes = 50
  )
)
```

# sp2rd

A simple R package to generate animated transitions between spatial locations
and reduced dimensional embeddings.

**This package is currently under development.**

## Installation

To install the development version:

```{r, eval = FALSE}
library(remotes)
install_github("BodenmillerGroup/sp2rd")
```

## Usage

The `sp2rd` function takes a `SingleCellExperiment` or `SpatialExperiment`
object as input. You will need to specify under which name the spatial 
coordinates are stored and which low dimensional embeding to project them
to:

```{r, message=FALSE}
options(timeout = 100000)
library(sp2rd)

spe <- readRDS(url("https://zenodo.org/record/7432486/files/spe.rds", "rb"))

# Select one image
cur_spe <- spe[,spe$sample_id == "Patient1_001"]

sp2rd(cur_spe, 
      coords = c("Pos_X", "Pos_Y"), 
      color_by = "celltype", 
      img_id = "sample_id", 
      dimred = "UMAP")
```

The animation can be saved using `anim_save("path/to/gif_name.gif")`.

## Maintainer

[Nils Eling](https://github.com/nilseling)

Owner

  • Name: BodenmillerGroup
  • Login: BodenmillerGroup
  • Kind: organization

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Dependencies

DESCRIPTION cran
  • SingleCellExperiment * imports
  • SpatialExperiment * imports
  • SummarizedExperiment * imports
  • dplyr * imports
  • gganimate * imports
  • ggplot2 * imports
  • magrittr * imports
  • methods * imports
  • scales * imports
  • tweenr * imports
  • knitr * suggests
  • markdown * suggests
  • rmarkdown * suggests
  • testthat * suggests