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style: better README
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@adrientaudiere
adrientaudiere committed Dec 12, 2023
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206 changes: 6 additions & 200 deletions README.md
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Expand Up @@ -51,117 +51,16 @@ if (!require("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("dada2")
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> CRAN: https://cloud.r-project.org
#> Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
#> Warning: package(s) not installed when version(s) same as or greater than current; use
#> `force = TRUE` to re-install: 'dada2'
#> Installation paths not writeable, unable to update packages
#> path: /usr/local/lib/R/site-library
#> packages:
#> BH, cpp11, httpgd, Rcpp, rlang, systemfonts
#> Old packages: 'ALDEx2', 'ANCOMBC', 'annotate', 'AnnotationDbi',
#> 'AnnotationHub', 'aricode', 'basilisk', 'basilisk.utils', 'BayesFactor',
#> 'beachmat', 'benchdamic', 'bibliometrix', 'BiocBaseUtils', 'BiocFileCache',
#> 'BiocGenerics', 'BiocNeighbors', 'BiocSingular', 'BiocVersion', 'Biostrings',
#> 'bluster', 'brio', 'bslib', 'Cairo', 'checkmate', 'ComplexHeatmap', 'copula',
#> 'covr', 'crosstalk', 'curl', 'data.table', 'dbplyr', 'dearseq', 'decontam',
#> 'DelayedMatrixStats', 'deldir', 'densvis', 'desc', 'DescTools', 'DESeq2',
#> 'dir.expiry', 'DirichletMultinomial', 'downloadthis', 'dqrng', 'drake', 'DT',
#> 'e1071', 'ecodist', 'edgeR', 'ExperimentHub', 'expm', 'fBasics', 'foreign',
#> 'fstcore', 'gaston', 'gdsfmt', 'genefilter', 'GenomeInfoDb', 'GenomicRanges',
#> 'gert', 'ggiraph', 'ggside', 'ggthemes', 'ggtree', 'ggtreeExtra', 'git2r',
#> 'gmp', 'graphlayouts', 'grImport2', 'gtools', 'haven', 'htmlTable',
#> 'htmlwidgets', 'httpuv', 'insight', 'interactiveDisplayBase', 'interp',
#> 'KEGGREST', 'later', 'lava', 'LEA', 'leaflet', 'leiden', 'limma', 'link2GI',
#> 'lintr', 'lme4', 'lpSolve', 'lpSolveAPI', 'Maaslin2', 'maps', 'markdown',
#> 'MAST', 'Matrix', 'MatrixModels', 'matrixStats', 'mclust', 'mia',
#> 'microbiome', 'microbiomeDataSets', 'MicrobiotaProcess',
#> 'MultiAssayExperiment', 'mvtnorm', 'network', 'nlme', 'NOISeq', 'ordinal',
#> 'osqp', 'pak', 'parameters', 'pcaPP', 'performance', 'plotrix', 'pls',
#> 'pracma', 'processx', 'progress', 'PROJ', 'qgraph', 'qs', 'R.utils',
#> 'rbibutils', 'RcppArmadillo', 'RcppEigen', 'Rdpack', 'report', 'Rfast',
#> 'rgl', 'rhdf5', 'rhdf5filters', 'rJava', 'Rmpfr', 'robustbase', 'rpart',
#> 'RSQLite', 'Rtsne', 's2', 'S4Vectors', 'sass', 'ScaledMatrix', 'scales',
#> 'scater', 'scuttle', 'segmented', 'SeqArray', 'seqinr', 'seriation',
#> 'Seurat', 'SeuratObject', 'shiny', 'shinybusy', 'SingleCellExperiment',
#> 'sna', 'sp', 'SparseArray', 'sparseMatrixStats', 'spatstat.data',
#> 'spatstat.explore', 'spatstat.linnet', 'spatstat.model', 'spatstat.random',
#> 'spatstat.sparse', 'spatstat.utils', 'spdep', 'stringdist', 'stringfish',
#> 'svglite', 'testthat', 'this.path', 'tinytex', 'TMB', 'treeio',
#> 'TreeSummarizedExperiment', 'units', 'V8', 'vroom', 'wesanderson', 'wk',
#> 'Wrench', 'XML', 'xml2', 'zCompositions', 'zinbwave', 'cluster'
BiocManager::install("phyloseq")
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> CRAN: https://cloud.r-project.org
#> Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
#> Warning: package(s) not installed when version(s) same as or greater than current; use
#> `force = TRUE` to re-install: 'phyloseq'
#> Installation paths not writeable, unable to update packages
#> path: /usr/local/lib/R/site-library
#> packages:
#> BH, cpp11, httpgd, Rcpp, rlang, systemfonts
#> Old packages: 'ALDEx2', 'ANCOMBC', 'annotate', 'AnnotationDbi',
#> 'AnnotationHub', 'aricode', 'basilisk', 'basilisk.utils', 'BayesFactor',
#> 'beachmat', 'benchdamic', 'bibliometrix', 'BiocBaseUtils', 'BiocFileCache',
#> 'BiocGenerics', 'BiocNeighbors', 'BiocSingular', 'BiocVersion', 'Biostrings',
#> 'bluster', 'brio', 'bslib', 'Cairo', 'checkmate', 'ComplexHeatmap', 'copula',
#> 'covr', 'crosstalk', 'curl', 'data.table', 'dbplyr', 'dearseq', 'decontam',
#> 'DelayedMatrixStats', 'deldir', 'densvis', 'desc', 'DescTools', 'DESeq2',
#> 'dir.expiry', 'DirichletMultinomial', 'downloadthis', 'dqrng', 'drake', 'DT',
#> 'e1071', 'ecodist', 'edgeR', 'ExperimentHub', 'expm', 'fBasics', 'foreign',
#> 'fstcore', 'gaston', 'gdsfmt', 'genefilter', 'GenomeInfoDb', 'GenomicRanges',
#> 'gert', 'ggiraph', 'ggside', 'ggthemes', 'ggtree', 'ggtreeExtra', 'git2r',
#> 'gmp', 'graphlayouts', 'grImport2', 'gtools', 'haven', 'htmlTable',
#> 'htmlwidgets', 'httpuv', 'insight', 'interactiveDisplayBase', 'interp',
#> 'KEGGREST', 'later', 'lava', 'LEA', 'leaflet', 'leiden', 'limma', 'link2GI',
#> 'lintr', 'lme4', 'lpSolve', 'lpSolveAPI', 'Maaslin2', 'maps', 'markdown',
#> 'MAST', 'Matrix', 'MatrixModels', 'matrixStats', 'mclust', 'mia',
#> 'microbiome', 'microbiomeDataSets', 'MicrobiotaProcess',
#> 'MultiAssayExperiment', 'mvtnorm', 'network', 'nlme', 'NOISeq', 'ordinal',
#> 'osqp', 'pak', 'parameters', 'pcaPP', 'performance', 'plotrix', 'pls',
#> 'pracma', 'processx', 'progress', 'PROJ', 'qgraph', 'qs', 'R.utils',
#> 'rbibutils', 'RcppArmadillo', 'RcppEigen', 'Rdpack', 'report', 'Rfast',
#> 'rgl', 'rhdf5', 'rhdf5filters', 'rJava', 'Rmpfr', 'robustbase', 'rpart',
#> 'RSQLite', 'Rtsne', 's2', 'S4Vectors', 'sass', 'ScaledMatrix', 'scales',
#> 'scater', 'scuttle', 'segmented', 'SeqArray', 'seqinr', 'seriation',
#> 'Seurat', 'SeuratObject', 'shiny', 'shinybusy', 'SingleCellExperiment',
#> 'sna', 'sp', 'SparseArray', 'sparseMatrixStats', 'spatstat.data',
#> 'spatstat.explore', 'spatstat.linnet', 'spatstat.model', 'spatstat.random',
#> 'spatstat.sparse', 'spatstat.utils', 'spdep', 'stringdist', 'stringfish',
#> 'svglite', 'testthat', 'this.path', 'tinytex', 'TMB', 'treeio',
#> 'TreeSummarizedExperiment', 'units', 'V8', 'vroom', 'wesanderson', 'wk',
#> 'Wrench', 'XML', 'xml2', 'zCompositions', 'zinbwave', 'cluster'

if (!require("devtools", quietly = TRUE)) {
install.packages("devtools")
}
#>
#> Attachement du package : 'devtools'
#> L'objet suivant est masqué depuis 'package:BiocManager':
#>
#> install
devtools::install_github("adrientaudiere/MiscMetabar")
#> Downloading GitHub repo adrientaudiere/MiscMetabar@HEAD
#> network (1.18.1 -> 1.18.2) [CRAN]
#> scales (1.2.1 -> 1.3.0 ) [CRAN]
#> sna (2.7-1 -> 2.7-2 ) [CRAN]
#> Installing 3 packages: network, scales, sna
#> Installation des packages dans '/tmp/RtmpVdTtbP/temp_libpathd6864a1812db'
#> (car 'lib' n'est pas spécifié)
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/tmp/RtmpOhxQ8G/remotes3c7b64ea9dfd3/adrientaudiere-MiscMetabar-d599627/DESCRIPTION’ ... OK
#> * preparing ‘MiscMetabar’:
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building ‘MiscMetabar_0.5.tar.gz’
#> Installation du package dans '/tmp/RtmpVdTtbP/temp_libpathd6864a1812db'
#> (car 'lib' n'est pas spécifié)
```

You can install the development version from
Expand All @@ -172,107 +71,16 @@ if (!require("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("dada2")
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> CRAN: https://cloud.r-project.org
#> Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
#> Warning: package(s) not installed when version(s) same as or greater than current; use
#> `force = TRUE` to re-install: 'dada2'
#> Installation paths not writeable, unable to update packages
#> path: /usr/local/lib/R/site-library
#> packages:
#> BH, cpp11, httpgd, Rcpp, rlang, systemfonts
#> Old packages: 'ALDEx2', 'ANCOMBC', 'annotate', 'AnnotationDbi',
#> 'AnnotationHub', 'aricode', 'basilisk', 'basilisk.utils', 'BayesFactor',
#> 'beachmat', 'benchdamic', 'bibliometrix', 'BiocBaseUtils', 'BiocFileCache',
#> 'BiocGenerics', 'BiocNeighbors', 'BiocSingular', 'BiocVersion', 'Biostrings',
#> 'bluster', 'brio', 'bslib', 'Cairo', 'checkmate', 'ComplexHeatmap', 'copula',
#> 'covr', 'crosstalk', 'curl', 'data.table', 'dbplyr', 'dearseq', 'decontam',
#> 'DelayedMatrixStats', 'deldir', 'densvis', 'desc', 'DescTools', 'DESeq2',
#> 'dir.expiry', 'DirichletMultinomial', 'downloadthis', 'dqrng', 'drake', 'DT',
#> 'e1071', 'ecodist', 'edgeR', 'ExperimentHub', 'expm', 'fBasics', 'foreign',
#> 'fstcore', 'gaston', 'gdsfmt', 'genefilter', 'GenomeInfoDb', 'GenomicRanges',
#> 'gert', 'ggiraph', 'ggside', 'ggthemes', 'ggtree', 'ggtreeExtra', 'git2r',
#> 'gmp', 'graphlayouts', 'grImport2', 'gtools', 'haven', 'htmlTable',
#> 'htmlwidgets', 'httpuv', 'insight', 'interactiveDisplayBase', 'interp',
#> 'KEGGREST', 'later', 'lava', 'LEA', 'leaflet', 'leiden', 'limma', 'link2GI',
#> 'lintr', 'lme4', 'lpSolve', 'lpSolveAPI', 'Maaslin2', 'maps', 'markdown',
#> 'MAST', 'Matrix', 'MatrixModels', 'matrixStats', 'mclust', 'mia',
#> 'microbiome', 'microbiomeDataSets', 'MicrobiotaProcess',
#> 'MultiAssayExperiment', 'mvtnorm', 'network', 'nlme', 'NOISeq', 'ordinal',
#> 'osqp', 'pak', 'parameters', 'pcaPP', 'performance', 'plotrix', 'pls',
#> 'pracma', 'processx', 'progress', 'PROJ', 'qgraph', 'qs', 'R.utils',
#> 'rbibutils', 'RcppArmadillo', 'RcppEigen', 'Rdpack', 'report', 'Rfast',
#> 'rgl', 'rhdf5', 'rhdf5filters', 'rJava', 'Rmpfr', 'robustbase', 'rpart',
#> 'RSQLite', 'Rtsne', 's2', 'S4Vectors', 'sass', 'ScaledMatrix', 'scales',
#> 'scater', 'scuttle', 'segmented', 'SeqArray', 'seqinr', 'seriation',
#> 'Seurat', 'SeuratObject', 'shiny', 'shinybusy', 'SingleCellExperiment',
#> 'sna', 'sp', 'SparseArray', 'sparseMatrixStats', 'spatstat.data',
#> 'spatstat.explore', 'spatstat.linnet', 'spatstat.model', 'spatstat.random',
#> 'spatstat.sparse', 'spatstat.utils', 'spdep', 'stringdist', 'stringfish',
#> 'svglite', 'testthat', 'this.path', 'tinytex', 'TMB', 'treeio',
#> 'TreeSummarizedExperiment', 'units', 'V8', 'vroom', 'wesanderson', 'wk',
#> 'Wrench', 'XML', 'xml2', 'zCompositions', 'zinbwave', 'cluster'
BiocManager::install("phyloseq")
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> CRAN: https://cloud.r-project.org
#> Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
#> Warning: package(s) not installed when version(s) same as or greater than current; use
#> `force = TRUE` to re-install: 'phyloseq'
#> Installation paths not writeable, unable to update packages
#> path: /usr/local/lib/R/site-library
#> packages:
#> BH, cpp11, httpgd, Rcpp, rlang, systemfonts
#> Old packages: 'ALDEx2', 'ANCOMBC', 'annotate', 'AnnotationDbi',
#> 'AnnotationHub', 'aricode', 'basilisk', 'basilisk.utils', 'BayesFactor',
#> 'beachmat', 'benchdamic', 'bibliometrix', 'BiocBaseUtils', 'BiocFileCache',
#> 'BiocGenerics', 'BiocNeighbors', 'BiocSingular', 'BiocVersion', 'Biostrings',
#> 'bluster', 'brio', 'bslib', 'Cairo', 'checkmate', 'ComplexHeatmap', 'copula',
#> 'covr', 'crosstalk', 'curl', 'data.table', 'dbplyr', 'dearseq', 'decontam',
#> 'DelayedMatrixStats', 'deldir', 'densvis', 'desc', 'DescTools', 'DESeq2',
#> 'dir.expiry', 'DirichletMultinomial', 'downloadthis', 'dqrng', 'drake', 'DT',
#> 'e1071', 'ecodist', 'edgeR', 'ExperimentHub', 'expm', 'fBasics', 'foreign',
#> 'fstcore', 'gaston', 'gdsfmt', 'genefilter', 'GenomeInfoDb', 'GenomicRanges',
#> 'gert', 'ggiraph', 'ggside', 'ggthemes', 'ggtree', 'ggtreeExtra', 'git2r',
#> 'gmp', 'graphlayouts', 'grImport2', 'gtools', 'haven', 'htmlTable',
#> 'htmlwidgets', 'httpuv', 'insight', 'interactiveDisplayBase', 'interp',
#> 'KEGGREST', 'later', 'lava', 'LEA', 'leaflet', 'leiden', 'limma', 'link2GI',
#> 'lintr', 'lme4', 'lpSolve', 'lpSolveAPI', 'Maaslin2', 'maps', 'markdown',
#> 'MAST', 'Matrix', 'MatrixModels', 'matrixStats', 'mclust', 'mia',
#> 'microbiome', 'microbiomeDataSets', 'MicrobiotaProcess',
#> 'MultiAssayExperiment', 'mvtnorm', 'network', 'nlme', 'NOISeq', 'ordinal',
#> 'osqp', 'pak', 'parameters', 'pcaPP', 'performance', 'plotrix', 'pls',
#> 'pracma', 'processx', 'progress', 'PROJ', 'qgraph', 'qs', 'R.utils',
#> 'rbibutils', 'RcppArmadillo', 'RcppEigen', 'Rdpack', 'report', 'Rfast',
#> 'rgl', 'rhdf5', 'rhdf5filters', 'rJava', 'Rmpfr', 'robustbase', 'rpart',
#> 'RSQLite', 'Rtsne', 's2', 'S4Vectors', 'sass', 'ScaledMatrix', 'scales',
#> 'scater', 'scuttle', 'segmented', 'SeqArray', 'seqinr', 'seriation',
#> 'Seurat', 'SeuratObject', 'shiny', 'shinybusy', 'SingleCellExperiment',
#> 'sna', 'sp', 'SparseArray', 'sparseMatrixStats', 'spatstat.data',
#> 'spatstat.explore', 'spatstat.linnet', 'spatstat.model', 'spatstat.random',
#> 'spatstat.sparse', 'spatstat.utils', 'spdep', 'stringdist', 'stringfish',
#> 'svglite', 'testthat', 'this.path', 'tinytex', 'TMB', 'treeio',
#> 'TreeSummarizedExperiment', 'units', 'V8', 'vroom', 'wesanderson', 'wk',
#> 'Wrench', 'XML', 'xml2', 'zCompositions', 'zinbwave', 'cluster'

if (!require("devtools", quietly = TRUE)) {
install.packages("devtools")
}
devtools::install_github("adrientaudiere/MiscMetabar", ref = "dev")
#> Downloading GitHub repo adrientaudiere/MiscMetabar@dev
#>
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> * checking for file ‘/tmp/RtmpOhxQ8G/remotes3c7b673226355/adrientaudiere-MiscMetabar-59ef25a/DESCRIPTION’ ... OK
#> * preparing ‘MiscMetabar’:
#> * checking DESCRIPTION meta-information ... OK
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building ‘MiscMetabar_0.51.tar.gz’
#> Installation du package dans '/tmp/RtmpVdTtbP/temp_libpathd6864a1812db'
#> (car 'lib' n'est pas spécifié)
```

## Some use of MiscMetabar
Expand All @@ -284,11 +92,11 @@ more examples.
For an introduction to metabarcoding in R, Please visite the [state of
the
field](https://adrientaudiere.github.io/MiscMetabar/articles/states_of_fields_in_R.html)
vignettes. The [import, export and track]() vignette explains how import
and export
<https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html>.
Its also show how to summarize useful information (number of sequences,
samples and clusters) accross bioinformatic pipelines.
vignettes. The [import, export and
track](https://adrientaudiere.github.io/MiscMetabar/articles/import_export_track.html)
vignette explains how import and export `phyloseq` object. Its also show
how to summarize useful information (number of sequences, samples and
clusters) accross bioinformatic pipelines.

If you are interested in ecological metrics, see the vignettes
describing
Expand All @@ -303,7 +111,7 @@ tutorial introduces the different way of clustering already-clustered
OTU/ASV. The vignette [tengeler]() explore the dataset from Tengeler et
al. (2020) using some MiscMetabar functions.

For developers, I also have a vignette describing som [rules of
For developers, I also wrote a vignette describing som [rules of
codes](https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html).

### Summarize a physeq object
Expand All @@ -322,8 +130,6 @@ summary_plot_pq(data_fungi)

``` r
p <- MiscMetabar::hill_pq(data_fungi, variable = "Height")
#> Taxa are now in rows.
#> Cleaning suppress 0 taxa and 0 samples.
p$plot_Hill_0
```

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