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small edits to the README to make it more compact and for readability
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cpauvert committed Sep 11, 2024
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<!-- README.md is generated from README.Rmd. Please edit that file -->

# maldipickr <a href="https://clavellab.github.io/maldipickr"><img src="man/figures/logo.svg" align="right" height="139" alt="maldipickr website" /></a>

<!-- badges: start -->

[![CRAN
status](https://www.r-pkg.org/badges/version/maldipickr)](https://CRAN.R-project.org/package=maldipickr)
status](https://www.r-pkg.org/badges/version/maldipickr.png)](https://CRAN.R-project.org/package=maldipickr)
[![Project Status: Active – The project has reached a stable, usable
state and is being actively
developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
Expand All @@ -23,100 +22,10 @@ developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.re
you dereplicate MALDI-TOF data and cherry-pick representative spectra of
microbial isolates.

## Graphical overview

<a href="https://raw.githubusercontent.com/ClavelLab/maldipickr/main/man/figures/maldipickr-data-flow-portrait.png"><img src="man/figures/maldipickr-data-flow-portrait-thumb.png" alt="Thumbnail of maldipickr graphical overview" /></a>

Illustration (click for a bigger version) of the data flow when using
`{maldipickr}` to cherry-pick bacterial isolates with MALDI Biotyper. It
depicts the two possible approaches using either taxonomic
identification reports (left) or spectra data (right).

## Quickstart

How to **cherry-pick bacterial isolates** with MALDI Biotyper:

- [using taxonomic identification
report](#using-taxonomic-identification-report)
- [using spectra data](#using-spectra-data)

### Using taxonomic identification report

``` r
library(maldipickr)
# Import Biotyper CSV report
# and glimpse at the table
report_tbl <- read_biotyper_report(
system.file("biotyper_unknown.csv", package = "maldipickr")
)
report_tbl %>%
dplyr::select(name, bruker_species, bruker_log)
#> # A tibble: 4 × 3
#> name bruker_species bruker_log
#> <chr> <chr> <dbl>
#> 1 unknown_isolate_1 not reliable identification 1.33
#> 2 unknown_isolate_2 not reliable identification 1.4
#> 3 unknown_isolate_3 Faecalibacterium prausnitzii 1.96
#> 4 unknown_isolate_4 Faecalibacterium prausnitzii 2.07


# Delineate clusters from the identifications after filtering the reliable ones
# and cherry-pick one representative spectra.
# The chosen ones are indicated by `to_pick` column
report_tbl <- report_tbl %>%
dplyr::mutate(
bruker_species = dplyr::if_else(bruker_log >= 2, bruker_species,
"not reliable identification")
)
report_tbl %>%
delineate_with_identification() %>%
pick_spectra(report_tbl, criteria_column = "bruker_log") %>%
dplyr::relocate(name, to_pick, bruker_species)
#> Generating clusters from single report
#> # A tibble: 4 × 11
#> name to_pick bruker_species membership cluster_size sample_name hit_rank
#> <chr> <lgl> <chr> <int> <int> <chr> <int>
#> 1 unknown_i… TRUE not reliable … 2 1 <NA> 1
#> 2 unknown_i… TRUE not reliable … 3 1 <NA> 1
#> 3 unknown_i… TRUE not reliable … 4 1 <NA> 1
#> 4 unknown_i… TRUE Faecalibacter… 1 1 <NA> 1
#> # ℹ 4 more variables: bruker_quality <chr>, bruker_taxid <dbl>,
#> # bruker_hash <chr>, bruker_log <dbl>
```

### Using spectra data

``` r
library(maldipickr)
# Set up the directory location of your spectra data
spectra_dir <- system.file("toy-species-spectra", package = "maldipickr")

# Import and process the spectra
processed <- spectra_dir %>%
import_biotyper_spectra() %>%
process_spectra()

# Delineate spectra clusters using Cosine similarity
# and cherry-pick one representative spectra.
# The chosen ones are indicated by `to_pick` column
processed %>%
list() %>%
merge_processed_spectra() %>%
coop::tcosine() %>%
delineate_with_similarity(threshold = 0.92) %>%
set_reference_spectra(processed$metadata) %>%
pick_spectra() %>%
dplyr::relocate(name, to_pick)
#> # A tibble: 6 × 7
#> name to_pick membership cluster_size SNR peaks is_reference
#> <chr> <lgl> <int> <int> <dbl> <int> <lgl>
#> 1 species1_G2 FALSE 1 4 5.09 21 FALSE
#> 2 species2_E11 FALSE 2 2 5.54 22 FALSE
#> 3 species2_E12 TRUE 2 2 5.63 23 TRUE
#> 4 species3_F7 FALSE 1 4 4.89 26 FALSE
#> 5 species3_F8 TRUE 1 4 5.56 25 TRUE
#> 6 species3_F9 FALSE 1 4 5.40 25 FALSE
```
> Check out the graphical overview (click for a bigger version).
> `{maldipickr}` can use two approaches:
> from taxonomic identification reports (left) or from spectra data (right).
> <a href="https://raw.githubusercontent.com/ClavelLab/maldipickr/main/man/figures/maldipickr-data-flow-portrait.png"><img src="man/figures/maldipickr-data-flow-portrait-thumb.png" alt="Thumbnail of maldipickr graphical overview" /></a>
## Installation

Expand All @@ -130,16 +39,26 @@ To install the latest CRAN release, use the following command in R:
install.packages("maldipickr")
```

Or if you are using [`{renv}`](https://cran.r-project.org/package=renv),
use:

``` r
renv::install("maldipickr")
```

To install the development version, use the following command in R:

``` r
remotes::install_github("ClavelLab/maldipickr", build_vignettes = TRUE)
# or with renv::install("ClavelLab/maldipickr")
```

## Usage

The comprehensive vignettes will walk you through the package functions
and showcase how to:
Start off with the [Introduction to
maldipickr](https://clavellab.github.io/maldipickr/articles/maldipickr.html)
for a quickstart. Otherwise, the comprehensive vignettes will walk you
through the package functions and showcase how to:

1. [Import spectra data and identification reports from Bruker MALDI
Biotyper into
Expand All @@ -148,33 +67,27 @@ and showcase how to:
simple to complex
design](https://clavellab.github.io/maldipickr/articles/dereplicate-bruker-maldi-biotyper-spectra.html).

## Troubleshoot
## Troubleshoot and Contribute

If something unexpected happened when using this package, please first
search the [current open or closed
**Troubleshoot** If something unexpected happened when using this
package, please first search the [current open or closed
issues](https://github.com/ClavelLab/maldipickr/issues?q=is%3Aissue++)
to look for similar problems. If you are the first, you are more than
welcome to open a new issue using the “Bug report” template with a
minimal [reprex](https://www.tidyverse.org/help/#reprex).

## Contribute

All contributions are welcome and the
**Contribute** All contributions are welcome and the
[`CONTRIBUTING.md`](https://clavellab.github.io/maldipickr/CONTRIBUTING.html)
documents how to participate.

Please note that the
documents how to participate. Please note that the
[`{maldipickr}`](https://github.com/ClavelLab/maldipickr) package is
released with a [Contributor Code of
Conduct](https://clavellab.github.io/maldipickr/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.

## Credits

### Acknowledgements

This R package is developed for spectra data generated by the Bruker
MALDI Biotyper device. The
**Acknowledgements** This R package is developed for spectra data
generated by the Bruker MALDI Biotyper device. The
[`{maldipickr}`](https://github.com/ClavelLab/maldipickr) package is
built from a suite of Rmarkdown files using the
[`{fusen}`](https://thinkr-open.github.io/fusen/) package by Rochette S
Expand All @@ -184,15 +97,12 @@ built from a suite of Rmarkdown files using the
package from Gibb & Strimmer (2012) for spectra functions
2. the work of Strejcek et al. (2018) for the dereplication procedure.

### Disclaimer

The developers of this package are part of the [Clavel
**Disclaimer** The developers of this package are part of the [Clavel
Lab](https://www.ukaachen.de/kliniken-institute/institut-fuer-medizinische-mikrobiologie/forschung/ag-clavel/)
and are not affiliated with the company Bruker, therefore this package
is independent of the company and is distributed under the [GPL-3.0
License](https://clavellab.github.io/maldipickr/LICENSE.html).

The hexagonal logo was created by Charlie Pauvert and uses the [Atkinson
License](https://clavellab.github.io/maldipickr/LICENSE.html). The
hexagonal logo was created by Charlie Pauvert and uses the [Atkinson
Hyperlegible
font](https://fonts.google.com/specimen/Atkinson+Hyperlegible/about)
font and a color palette generated at
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