-
Notifications
You must be signed in to change notification settings - Fork 1
/
README.Rmd
174 lines (126 loc) · 7.8 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
---
output: github_document
always_allow_html: yes
bibliography: paper/bibliography.bib
---
![R](https://img.shields.io/badge/r-%23276DC3.svg?style=for-the-badge&logo=r&logoColor=white)
<a href="https://zenodo.org/badge/latestdoi/268765075"><img src="https://zenodo.org/badge/268765075.svg" alt="DOI"></a>
[![codecov](https://codecov.io/gh/adrientaudiere/MiscMetabar/graph/badge.svg?token=NXFRSIKYC0)](https://app.codecov.io/gh/adrientaudiere/MiscMetabar)
[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](https://github.com/adrientaudiere/MiscMetabar/blob/master/CODE_OF_CONDUCT.md)
[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
[![CodeFactor](https://www.codefactor.io/repository/github/adrientaudiere/miscmetabar/badge/master)](https://www.codefactor.io/repository/github/adrientaudiere/miscmetabar/overview/master)
[![R-CMD-check](https://github.com/adrientaudiere/MiscMetabar/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/adrientaudiere/MiscMetabar/actions/workflows/R-CMD-check.yaml)
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06038/status.svg)](https://doi.org/10.21105/joss.06038)
<!-- README.md is generated from README.Rmd. Please edit that file -->
<!-- devtools::build_readme() -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%",
message = FALSE
)
```
# MiscMetabar <a href="https://adrientaudiere.github.io/MiscMetabar/"><img src="https://adrientaudiere.github.io/MiscMetabar/reference/figures/logo.png" align="right" height="138" alt="MiscMetabar website" /></a>
See the pkgdown documentation site [here](https://adrientaudiere.github.io/MiscMetabar/) and the [package paper](https://doi.org/10.21105/joss.06038) in the Journal Of Open Softwares.
Biological studies, especially in ecology, health sciences and taxonomy, need to describe the biological composition of samples. Over the last twenty years, (i) the development of DNA sequencing, (ii) reference databases, (iii) high-throughput sequencing (HTS), and (iv) bioinformatics resources have enabled the description of biological communities through metabarcoding. Metabarcoding involves the sequencing of millions (*meta*-) of short regions of specific DNA (*-barcoding*, @valentini2009) often from environmental samples (eDNA, @taberlet2012) such as human stomach contents, lake water, soil, and air.
`MiscMetabar` aims to facilitate the **description**, **transformation**, **exploration** and **reproducibility** of metabarcoding analyses using R. The development of `MiscMetabar` relies heavily on the R packages [`dada2`](https://benjjneb.github.io/dada2/index.html) [@callahan2016], [`phyloseq`](https://joey711.github.io/phyloseq/) [@mcmurdie2013] and [`targets`](https://books.ropensci.org/targets/) [@landau2021].
## Installation
A CRAN version of MiscMetabar is available.
```{r, results = 'hide', eval=FALSE}
install.packages("MiscMetabar")
```
You can also install the stable development version from [GitHub](https://github.com/) with:
```{r, results = 'hide', eval=FALSE}
if (!require("devtools", quietly = TRUE)) {
install.packages("devtools")
}
devtools::install_github("adrientaudiere/MiscMetabar")
```
You can install the unstable development version from [GitHub](https://github.com/) with:
```{r, results = 'hide', eval=FALSE}
if (!require("devtools", quietly = TRUE)) {
install.packages("devtools")
}
devtools::install_github("adrientaudiere/MiscMetabar", ref = "dev")
```
## Some use of MiscMetabar
See articles in the [MiscMetabar](https://adrientaudiere.github.io/MiscMetabar/) website for more examples.
For an introduction to metabarcoding in R, see the [state of the field](https://adrientaudiere.github.io/MiscMetabar/articles/states_of_fields_in_R.html) article. The [import, export and tracking](https://adrientaudiere.github.io/MiscMetabar/articles/import_export_track.html) article explains how to import and export `phyloseq` objects. It also shows how to summarize useful information (number of sequences, samples and clusters) across bioinformatic pipelines. The article [explore data](https://adrientaudiere.github.io/MiscMetabar/articles/explore_data.html) takes a closer look at different ways to explore samples and taxonomic data from `phyloseq` object.
If you are interested in ecological metrics, see the articles describing [alpha-diversity](https://adrientaudiere.github.io/MiscMetabar/articles/alpha-div.html) and [beta-diversity](https://adrientaudiere.github.io/MiscMetabar/articles/beta-div.html) analysis.
The article [filter taxa and samples](https://adrientaudiere.github.io/MiscMetabar/articles/filter.html) describes some data filtering processes using MiscMetabar and the [reclustering](https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html) tutorial introduces the different way of clustering already-clustered OTU/ASV. The article [tengeler](https://adrientaudiere.github.io/MiscMetabar/articles/tengeler.html) explore the dataset from Tengeler et al. (2020) using some MiscMetabar functions.
For developers, I also wrote an article describing some [rules of codes](https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html).
### Summarize a physeq object
```{r example}
library("MiscMetabar")
library("phyloseq")
library("magrittr")
data("data_fungi")
summary_plot_pq(data_fungi)
```
### Alpha-diversity analysis
```{r, fig.cap="Hill number 1"}
p <- MiscMetabar::hill_pq(data_fungi, fact = "Height")
p$plot_Hill_0
```
```{r, fig.cap="Result of the Tuckey post-hoc test"}
p$plot_tuckey
```
### Beta-diversity analysis
```{r}
if (!require("ggVennDiagram", quietly = TRUE)) {
install.packages("ggVennDiagramà")
}
ggvenn_pq(data_fungi, fact = "Height") +
ggplot2::scale_fill_distiller(palette = "BuPu", direction = 1) +
labs(title = "Share number of ASV among Height in tree")
```
### Note for non-Linux users
Some functions may not work on Windows (*e.g.* `track_wflow()`, `cutadapt_remove_primers()`, `krona()`, `vsearch_clustering()`, ...). A solution is to exploit docker container, for example the using the great [rocker project](https://rocker-project.org/).
Here is a list of functions with some limitations or not working at all on Windows OS:
- `build_phytree_pq()`
- `count_seq()`
- `cutadapt_remove_primers()`
- `krona()`
- `merge_krona()`
- `multipatt_pq()`
- `plot_tsne_pq()`
- `rotl_pq()`
- `save_pq()`
- `tax_datatable()`
- `track_wkflow()`
- `track_wkflow_samples()`
- `tsne_pq()`
- `venn_pq()`
MiscMetabar is developed under Linux and the vast majority of functions may works on Unix system, but its functionning is not tested under iOS.
### Installation of other softwares for Debian Linux distributions
If you encounter any errors or have any questions about the installation of these softwares, please visit their dedicated websites.
#### [blast+](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html#downloadblastdata)
```sh
sudo apt-get install ncbi-blast+
```
#### [vsearch](https://github.com/torognes/vsearch)
```sh
sudo apt-get install vsearch
```
An other possibilities is to [install vsearch](https://bioconda.github.io/recipes/vsearch/README.html?highlight=vsearch#package-package%20'vsearch') with `conda`.
#### [swarm](https://github.com/torognes/swarm)
```sh
git clone https://github.com/torognes/swarm.git
cd swarm/
make
```
An other possibilities is to [install swarm](https://bioconda.github.io/recipes/swarm/README.html?highlight=swarm#package-package%20'swarm') with `conda`.
#### [Mumu](https://github.com/frederic-mahe/mumu)
```sh
git clone https://github.com/frederic-mahe/mumu.git
cd ./mumu/
make
make check
make install # as root or sudo
```
#### [cutadapt](https://cutadapt.readthedocs.io/en/stable/)
```sh
conda create -n cutadaptenv cutadapt
```