README.Rmd

---
output: github_document
editor_options: 
  chunk_output_type: console
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<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, echo = FALSE, message = FALSE, error = FALSE, warning = FALSE}
library(tidyverse)
library(dynmethods)

load("data/methods.rda")
```


<img src="man/figures/logo.png" align="right" /> [![Build status](https://travis-ci.org/dynverse/dynmethods.svg?branch=master)](https://travis-ci.org/dynverse/dynmethods)

# A collection of `r nrow(methods)` trajectory inference methods
This package contains wrappers for all of the trajectory inference (TI) methods included in the [dynverse](https://www.github.com/dynverse/dynverse) review. The output of each method is transformed into a common trajectory model using [dynwrap](https://www.github.com/dynverse/dynwrap). Nearly all methods are integrated within a docker container, avoiding dependency issues. Some methods are also directly wrapped inside of R.

**To run any of these methods, interpret the results and visualise the trajectory, see the [dyno package](https://www.github.com/dynverse/dyno).**

To include your own method, feel free to send us a [pull request](https://github.com/dynverse/dynmethods/pulls) or create an [issue](https://github.com/dynverse/dynmethods/labels/new%20method). The easiest way to add a new method is [through a docker container](https://dynverse.github.io/dynwrap/articles/create_ti_method_docker.html), so that dependencies don't pose any issues for other users, but we also welcome methods [directly wrapped inside of R](https://dynverse.github.io/dynwrap/articles/create_ti_method_r.html). The main benefit of adding your own method is that users can easily compare your method with others and [visualise/interpret the output](https://www.github.com/dynverse/dyno). Moreover, your method will be compared to other methods within [the TI method evaluation](https://doi.org/10.1101/276907).

Currently wrapped are the following methods:

```{r, echo = FALSE, warning = FALSE, error = FALSE, message = FALSE, results='asis'}
df <- methods %>% 
  arrange(name) %>% 
  arrange(fct_infreq(type)) %>% 
  mutate(
    code_label = wrapper_location,
    code_url = glue::glue("https://github.com/dynverse/dynmethods/blob/master/{wrapper_location}"),
    r_wrapper_url = glue::glue("https://github.com/dynverse/dynmethods/blob/master/{r_wrapper_location}"),
    docker_url = glue::glue("https://github.com/dynverse/dynmethods/blob/master/{docker_wrapper_location}"),
    Wrapper = glue::glue("[{code_label}]({code_url})"),
    vignette_label = glue::glue("{method_id}.md"),
    vignette_relpath = glue::glue("inst/doc/{vignette_label}"),
    vignette_url = glue::glue("https://github.com/dynverse/dynmethods/blob/master/{vignette_relpath}"),
    Vignette = ifelse(file.exists(vignette_relpath), glue::glue("[{vignette_label}]({vignette_url})"), ""),
    `Method` = map2_chr(name, doi, function(name, doi) {
      if (!is.null(doi) && !is.na(doi)) {
        glue::glue("{name} <a href='https://doi.org/{doi}'><img src='man/figures/doi_logo.png' height='16'></a>")
      } else {
        name
      }
    }),
    `R wrapper` = ifelse(
      r_wrapped,
      glue::glue("✓ ([code]({r_wrapper_url}))"),
      ""
    ),
    `Docker container` = ifelse(
      containerised, 
      glue::glue("✓ ([code]({docker_url}), [dockerhub]({dockerhub_url}))"), 
      ""
    ),
    `Authors` = map_chr(authors, function(authors) {
      map_chr(authors, function(author) {
        if (is.null(author$family)) {
          author$family <- ""
        }
        author_text <- glue::glue("{author$given} {author$family}")
        
        if (!is.null(author$ORCID)) {
          author_text <- glue::glue("{author_text} <a href='https://orcid.org/{author$ORCID}'><img src='man/figures/orcid_logo.svg' height='16'></a>")
        }
        
        if (!is.null(author$github)) {
          author_text <- glue::glue("{author_text} <a href='https://github.com/{author$github}'><img src='man/figures/github_logo.png' height='16'></a>")
        }
        
        author_text %>% paste0("<sub>", ., "</sub>")
      }) %>% glue::collapse("<br>")
    })
  )

df2 <- df %>% 
  select(
    `Method`,
    Wrapper, 
    `<a href='https://github.com/dynverse/dynmethods/tree/master/R'><img src='man/figures/r_logo.png' height='30'></a>` = `R wrapper`, 
    `<a href='https://hub.docker.com/u/dynverse/'><img src='man/figures/docker_logo.png' height='30'></a>` = `Docker container`,
    `Authors`
  )

knitr::kable(df2)
```