https://github.com/patzaw/glossary

Simple glossary management for R/Rmd
https://github.com/patzaw/glossary

Last synced: about 2 months ago
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Simple glossary management for R/Rmd

• Host: GitHub
• URL: https://github.com/patzaw/glossary
• Owner: patzaw
• Created: 2021-04-23T06:56:40.000Z (over 3 years ago)
• Default Branch: master
• Last Pushed: 2021-04-30T12:48:33.000Z (over 3 years ago)
• Last Synced: 2024-08-13T07:11:36.210Z (5 months ago)
• Language: R
• Size: 5.86 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.Rmd

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• jimsghstars - patzaw/glossary - Simple glossary management for R/Rmd (R)

README

        
---

title: "README"

output:

  md_document:

    variant: gfm

    toc: true

    toc_depth: 2

editor_options: 

  chunk_output_type: console

---

```{r setup, include = FALSE}

library(knitr)

```

# Introduction

This small script allows the management of simple glossaries.

## Dependencies

This script depends on the following packages:

```{r, include=FALSE}

library(magrittr)

library(dplyr)

library(glue)

library(reactable)

```

```{r, eval=FALSE}

library(magrittr)

library(dplyr)

library(glue)

library(reactable)

```

# Use

## Load and create a glossary

```{r}

source("glossary.R")

glossary <- create_glossary()

```

## Add terms in the glossary

```{r}

glossary$add_term(

   "UMI",

   "Unique Molecular Identifier. Each PCR primer is associated to a UMI to identify PCR duplicates when quantifying the transcripts. Therefore the number of counts corresponds to the number of UMI which is the quantification measure per feature."

)

```

Synonyms can also be provided:

```{r}

glossary$add_term(

   "MT",

   "Genes coded by mitochondrial genome. MT (%) corresponds to the percentage of UMI corresponding to mitochondrial genes."

)

glossary$add_synonyms("MT", "MT (%)")

```

## Showing the glossary

- `glossary$get_table()` returns the glossary tibble

- `glossary$view()` shows the glossary in a reactable

## Get definitions

The following function is used to get the definitions of terms of interest.

It's case insensitive and support plurals by default.

```{r}

glossary$get_definitions(c("mt", "UMIs"))

```

In an markdown or html document, the definitions can be shown in tooltips

using the `glossary$get_html_definitions()` function.

For example: `r glossary$get_html_definitions("UMIs")`.

CSS style can be customized using the `style` parameter

(Unfortunately, CSS are not rendered in GitHub markdown as it is a part of the

sanitization process).

To make it easier to use in an Rmd document in RStudio this function can

be copied in a function with a shorter name such as:

```{r}

td <- glossary$get_html_definitions

```

And then the following

markdown [snippet](https://support.rstudio.com/hc/en-us/articles/204463668-Code-Snippets)

can be added in RStudio (Edit Snippets button in Global Options -> Code):

```

snippet td

	`r${2} td(${1})`

```