Commit 9e4d5d1b authored by mahendra-mariadassou's avatar mahendra-mariadassou
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add readme

parent e6d5d708
......@@ -19,37 +19,34 @@ knitr::opts_chunk$set(
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
<!-- badges: end -->
The goal of affiliationExplorer is to ...
The goal of affiliationExplorer is to provide a user-friendly graphical interface to choose between different conflicting affiliations.
## Installation
You need to provide to upload two files to the application:
You can install the released version of affiliationExplorer from [CRAN](https://CRAN.R-project.org) with:
- a `biom` file
- a multihits file (typically called `multihits_blabla.tsv`)
``` r
install.packages("affiliationExplorer")
```
The app will then sort the multi-affiliated taxa from most abundant to least abundant and help you pick one (or none) of the conflicting affiliations. You can also edit the affiliation manually.
## Example
Finally, use the `Download` button to download the biom file with corrected affiliations. This cleaned biom can be parsed with `import_frogs()` from the `phyloseq.extended` [package](https://github.com/mahendra-mariadassou/phyloseq-extended/tree/dev)
This is a basic example which shows you how to solve a common problem:
**Note** `affiliationExplorer` uses short taxa names, which may differ from the original names, in the display. However, names from the original biom file are preserved in the cleaned biom.
```{r example}
library(affiliationExplorer)
## basic example code
```
## Installation
What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:
You can install the latest version of `affiliationExplorer` from [github](https://github.com/mahendra-mariadassou/affiliationExplorer) with:
```{r cars}
summary(cars)
``` r
## install.packages("remotes")
remotes::install_github("mahendra-mariadassou/affiliationExplorer")
```
You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date.
## Launching the app
You can also embed plots, for example:
You can launch on your computer as follows:
```{r pressure, echo = FALSE}
plot(pressure)
```{r example, eval = FALSE}
library(affiliationExplorer)
affiliationExplorer::run_app()
```
In that case, don't forget to commit and push the resulting figure files, so they display on GitHub!
<!-- README.md is generated from README.Rmd. Please edit that file -->
# affiliationExplorer
<!-- badges: start -->
[![Lifecycle:
experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
<!-- badges: end -->
The goal of affiliationExplorer is to provide a user-friendly graphical
interface to choose between different conflicting affiliations.
You need to provide to upload two files to the application:
- a `biom` file
- a multihits file (typically called `multihits_blabla.tsv`)
The app will then sort the multi-affiliated taxa from most abundant to
least abundant and help you pick one (or none) of the conflicting
affiliations. You can also edit the affiliation manually.
Finally, use the `Download` button to download the biom file with
corrected affiliations. This cleaned biom can be parsed with
`import_frogs()` from the `phyloseq.extended`
[package](https://github.com/mahendra-mariadassou/phyloseq-extended/tree/dev)
**Note** `affiliationExplorer` uses short taxa names, which may differ
from the original names, in the display. However, names from the
original biom file are preserved in the cleaned biom.
## Installation
You can install the latest version of `affiliationExplorer` from
[github](https://github.com/mahendra-mariadassou/affiliationExplorer)
with:
``` r
## install.packages("remotes")
remotes::install_github("mahendra-mariadassou/affiliationExplorer")
```
## Launching the app
You can launch on your computer as follows:
``` r
library(affiliationExplorer)
affiliationExplorer::run_app()
```
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