From d59ec9111ae8a733b323ace9aea797b181c47cfd Mon Sep 17 00:00:00 2001 From: Adrien Taudiere <6680165+adrientaudiere@users.noreply.github.com> Date: Wed, 6 Dec 2023 14:20:15 +0100 Subject: [PATCH 1/9] Update paper.md --- paper/paper.md | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index 1d5116af..f3f96df2 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -20,13 +20,13 @@ bibliography: paper.bib --- # Summary -Describing communities of living organisms increasingly relies on massive DNA sequencing from environmental samples (e-DNA). The analysis of these large amounts of sequences is well established in the R ecosystem, especially for metabarcoding, i.e. the massive sequencing of a given DNA region, called markers. The `MiscMetabar` package aims to facilitate the *description*, *transformation*, *exploration*, and *reproducibility* of metabarcoding analysis. Several tutorials are available [online](https://adrientaudiere.github.io/MiscMetabar/articles/). +Describing communities of living organisms increasingly relies on massive DNA sequencing from environmental samples (e-DNA). The analysis of these large amounts of sequences is well established in the R ecosystem, especially for metabarcoding, i.e. the massive sequencing of one or several given DNA regions, called markers. The `MiscMetabar` package aims to facilitate the *description*, *transformation*, *exploration*, and *reproducibility* of metabarcoding analysis. Several tutorials are available [online](https://adrientaudiere.github.io/MiscMetabar/articles/). # Statement of Need Biological studies, especially in ecology, health sciences and taxonomy, need to describe the biological composition of samples. During the last twenty years, the development of (i) high-throughput DNA sequencing, (ii) reference databases and (iii) bioinformatics resources have allowed 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. -Several plateforms (referenced in @tedersoo2022) such as QIIME2 [@bolyen2019], mothur [@schloss2020], and Galaxy [@jalili2020] allow complete analysis from raw fastq sequences to statistical analysis and visualization. However, the R ecosystem [@rcran], is very rich (Table 1) and more flexible than these platforms. +Several platforms (referenced in @tedersoo2022) such as QIIME2 [@bolyen2019], mothur [@schloss2020], and Galaxy [@jalili2020] allow complete analysis from raw fastq sequences to statistical analysis and visualization. However, the R ecosystem [@rcran], is very rich (fig. 1) and more flexible than these platforms. `MiscMetabar` aims to facilitate the **description**, **transformation**, **exploration** and **reproducibility** of metabarcoding analysis using R. The development of `MiscMetabar` relies heavily on the R packages `dada2`, `phyloseq` and `targets`. @@ -36,7 +36,7 @@ The metabarcoding ecosystem in the R language is mature, well-constructed, and r R package [`dada2`](http://bioconductor.org/packages/release/bioc/html/dada2.html) [@callahan2016] provides a highly cited and recommended clustering method [@pauvert2019]. [`phyloseq`](http://bioconductor.org/packages/release/bioc/html/phyloseq.html) [@mcmurdie2013] facilitate metagenomics analysis by providing a way to store data (the `phyloseq` class) and provides graphical and statistical functions. `MiscMetabar` is based on the `phyloseq` class from `phyloseq`, the most cited package in metagenomics [@wen2023]. For a description and comparison of other integrated packages competing with phyloseq, see @wen2023. Some packages already extend the phyloseq packages, in particular [`microbiome`](https://microbiome.github.io/) package collection [@ernst2023], the `speedyseq` package [@mclaren2020] and the package [phylosmith](https://schuyler-smith.github.io/phylosmith/) [@smith2019]. -![Table 1 : Important functions of MiscMetabar with their equivalent when available in other R packages: 1. Mia [@ernst2023]; 2. microViz [@Barnett2021]; 3. MicrobiotaProcess [@xu2023]; 4 Phylosmith [@smith2019].](figures_svg/table1.svg){width="100%"} +![Important functions of MiscMetabar with their equivalent when available in other R packages: 1. Mia [@ernst2023]; 2. microViz [@Barnett2021]; 3. MicrobiotaProcess [@xu2023]; 4 Phylosmith [@smith2019].](figures_svg/table1_publication.svg){width="100%"} `MiscMetabar` enriches this R ecosystem by providing functions to (i) **describe** your dataset visually, (ii) **transform** your data, (iii) **explore** biological diversity (alpha, beta, and taxonomic diversity), and (iv) simplify **reproducibility**. `MiscMetabar` is already used by the scientific community in several teams [@Vieira2021; @Pleic2022; @McCauley2022; @McCauley2023; @bouilloud2023; @vieira2023]. @@ -44,7 +44,8 @@ R package [`dada2`](http://bioconductor.org/packages/release/bioc/html/dada2.htm ## Description -A quick graphical representation of the phyloseq object is available using the `summary_plot_pq()` function (fig. 1A). This plot allows the novice to understand the structure of a phyloseq object and contains useful information The functions `krona()` and `tax_datatable()` describe the taxonomy of organisms using krona interactive pie chart [@ondov2011] and [datatable](https://datatables.net/) libraries, respectively. +A quick graphical representation of the phyloseq object is available using the `summary_plot_pq()` function (fig. 2A). +This plot provides an information-rich structural overview of the phyloseq object. The functions `krona()` and `tax_datatable()` describe the taxonomy of organisms using krona interactive pie chart [@ondov2011] and [datatable](https://datatables.net/) libraries, respectively. ## Transformation @@ -52,21 +53,21 @@ A quick graphical representation of the phyloseq object is available using the ` The function `clean_pq()` validates a phyloseq object, mainly by removing empty taxa and samples, and checking for discrepancies between taxa and sample names in different slots. -The filter functions `subset_samples_pq()` and `subset_taxa_pq()` complement `phyloseq::subset_samples()` and `phyloseq::subset_taxa()`, allowing the use of a boolean vector to filter samples or taxa from a phyloseq object. +The filter functions `subset_samples_pq()` and `subset_taxa_pq()` complement `subset_samples()` and `subset_taxa()` from the [`phyloseq`](http://bioconductor.org/packages/release/bioc/html/phyloseq.html) package, allowing the use of a boolean vector to filter samples or taxa from a phyloseq object. I also implement a function to filter taxa based on their blast to a custom database (`filter_asv_blast()`). This function uses the blastn software [@altschul1990] to compare ASV sequences to a database and filter out species that are below a given threshold of e-value and/or bit-score. ### Post-clustering -Several pipeline use at least two step of clustering. The function `asv2otu()`, using either the `DECIPHER::Clusterize()` function from R or the [vsearch](https://github.com/torognes/vsearch) software allow to recluster existing groups such as **ASV** (stands for *Amplicon Sequence Variant*) obtained by the `dada2::dada()` function (see the vignette [reclustering](https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html)). Another transformation method is implemented in `lulu_pq()`, which uses @froslev2017's method for post-clustering curation of DNA amplicon data. +Several pipelines use at least two step of clustering. The function `asv2otu()`, using either the `DECIPHER::Clusterize()` function from R or the [vsearch](https://github.com/torognes/vsearch) software allow to recluster existing groups such as **ASV** (stands for *Amplicon Sequence Variant*) obtained by the `dada2::dada()` function (see the vignette [reclustering](https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html)). Another transformation method is implemented in `lulu_pq()`, which uses @froslev2017's method for post-clustering curation of DNA amplicon data. Note that a fast and robust C++ re-implementation of lulu called [mumu](https://github.com/frederic-mahe/mumu) [@mahe2023] is also available through the function `mumu_pq()`. ## Exploration `MiscMetabar` provides a large number of facilities to explore the biological diversity in a phyloseq object. In most functions, a parameter enables the effect of the number of reads (sampling depth) to be controlled by rarefaction or other statistical methods, depending on the function. For example, the alpha diversity analysis (function `hill_pq()`) uses the HSD-Tuckey test on a linear model that includes the square roots of the number of reads as the first explanatory variable. -To illustrate the effect of sample variables on the taxonomy, `MiscMetabar` provides the functions `treemap_pq()`, `multitax_bar_pq()` (fig. 1D) and `heat_tree_pq()` (fig. 1E). The effect of an environmental variable (beta-diversity) on a biological organism can be explored by upset plot (`pset_pq()`; fig. 1F), venn diagram (`ggvenn_pq()`; fig. 1G), and circle plot (`circle_pq()`). This effect can be tested with PERMANOVA (`adonis_pq()`) and the network test (`graph_test_pq()`). If only two modalities are compared, `biplot_pq()` is very useful (fig. 1H). Differential abundance analysis can be performed directly using the `plot_deseq2_pq()` function (fig. 1I). +To illustrate the effect of sample variables on the taxonomy, `MiscMetabar` provides the functions `treemap_pq()`, `multitax_bar_pq()` (fig. 2D) and `heat_tree_pq()` (fig. 2E). The effect of an environmental variable (beta-diversity) on a biological organism can be explored by upset plot (`pset_pq()`; fig. 2F), venn diagram (`ggvenn_pq()`; fig. 2G), and circle plot (`circle_pq()`). This effect can be tested with PERMANOVA (`adonis_pq()`) and the network test (`graph_test_pq()`). If only two modalities are compared, `biplot_pq()` is very useful (fig. 2H). Differential abundance analysis can be performed directly using the `plot_deseq2_pq()` function (fig. 2I). -![Figure 1 : Some illustrations from MiscMetabar with the tengeler dataset from mia R package](figures_svg/tengeler_MiscMetabar.svg) +![Some illustrations from MiscMetabar with the tengeler dataset from mia R package](figures_svg/tengeler_MiscMetabar.svg) ## Reproducibility @@ -76,4 +77,4 @@ The targets R package [@Landau2021] improves the efficiency and reproducibility I thank Will Landau, Paul McMurdie, and Benjamin Callahan for their excellent R packages on which `MiscMetabar` rests. I also want to acknowledge Franck Richard, Lise Roy, Élisa Taschen and the [Mycea](https://mycea.fr/) team for the discussion and work around metabarcoding. -# References \ No newline at end of file +# References From 8ef7b78dff9ec6bb3a7315aafcd9ed8e8534d4d0 Mon Sep 17 00:00:00 2001 From: Adrien Taudiere <6680165+adrientaudiere@users.noreply.github.com> Date: Wed, 6 Dec 2023 14:20:35 +0100 Subject: [PATCH 2/9] Update paper.bib --- paper/paper.bib | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/paper/paper.bib b/paper/paper.bib index 2b1da104..ea3e94ea 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -1,4 +1,4 @@ -@article{altschul1990, +@article{altschul1990, doi = {10.32388/rhq6vj}, title = {Basic local alignment search tool}, author = {Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J}, @@ -101,6 +101,14 @@ @article{Landau2021 url = {https://doi.org/10.21105/joss.02959} } +@software{mahe2023, + url = {https://github.com/frederic-mahe/mumu/}, + year = {2023}, + version = {1.0.2}, + author = {Frédéric Mahé}, + title = {mumu: post-clustering curation tool for metabarcoding data} +} + @article{McCauley2022, author = {McCauley, Mark and Goulet, Tamar and Jackson, Colin and Loesgen, Sandra}, journal = {Research Square}, @@ -133,7 +141,6 @@ @software{mclaren2020 doi = {10.5281/zenodo.3923184}, url = {https://doi.org/10.5281/zenodo.3923184} } - @article{mcmurdie2013, doi = {10.1371/journal.pone.0061217}, author = {Paul J. McMurdie and Susan Holmes}, @@ -145,7 +152,8 @@ @article{mcmurdie2013 year = {2013}, url = {http://dx.plos.org/10.1371/journal.pone.0061217} } -@article{ondov2011, + + @article{ondov2011, title = {Interactive metagenomic visualization in a Web browser}, author = {Ondov, Brian D and Bergman, Nicholas H and Phillippy, Adam M}, journal = {BMC bioinformatics}, @@ -156,7 +164,7 @@ @article{ondov2011 publisher = {BioMed Central} } - @article{pauvert2019, +@article{pauvert2019, doi = {10.1016/j.funeco.2019.03.005}, title = {Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline}, author = {Pauvert, Charlie and Bu{\'e}e, Marc and Laval, Val{\'e}rie and Edel-Hermann, V{\'e}ronique and Fauchery, Laure and Gautier, Ang{\'e}lique and Lesur, Isabelle and Vallance, Jessica and Vacher, Corinne}, @@ -203,7 +211,7 @@ @article{schloss2020 publisher = {Am Soc Microbiol} } -@article{Smith2019, +@article{smith2019, doi = {10.21105/joss.01442}, url = {https://doi.org/10.21105/joss.01442}, year = {2019}, @@ -292,4 +300,4 @@ @article{xu2023 number = {2}, year = {2023}, publisher = {Elsevier} -} \ No newline at end of file +} From 2bce923cfff87774ad93d36a3b7d58efd0eb93b8 Mon Sep 17 00:00:00 2001 From: Adrien Taudiere <6680165+adrientaudiere@users.noreply.github.com> Date: Wed, 6 Dec 2023 14:24:04 +0100 Subject: [PATCH 3/9] Minor changes in figures --- paper/table1_publication.svg | 1570 ++++ paper/tengeler_MiscMetabar.svg | 12387 +++++++++++++++++++++++++++++++ 2 files changed, 13957 insertions(+) create mode 100644 paper/table1_publication.svg create mode 100644 paper/tengeler_MiscMetabar.svg diff --git a/paper/table1_publication.svg b/paper/table1_publication.svg new file mode 100644 index 00000000..6da525dc --- /dev/null +++ b/paper/table1_publication.svg @@ -0,0 +1,1570 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MiscMetabar + + + Other packages + + + 1. Mia — 2. microViz — 3.MicrobiotaProcess — 4. Phylosmith + + + Conversion to physeq + + + Conversion from physeq + + + Describe + + + summary_plot_pq() + + + krona() + + + sankey_pq() + + + accu_plot() + + + SRS_curve_pq() + + + clean_pq() + + + filter_asv_blast() + + + asv2otu() + + + lulu_pq() + + + E + x + p + l + o + r + e + + + Alpha-diversity + + + hill_pq() + + + Beta-diversity + + + ggvenn_pq() + + + upset_pq() + + + graph_test_pq() + + + adonis_pq() + + + plot_tsne_pq() + + + plot_tax_pq() + + + circle_pq() + + + amplicon::tax_circlize() + + + Compare 2 modalities + + + biplot_pq() + + + compare_pairs_pq() + + + Differential abundance + + + plot_deseq2_pq() + + + Taxonomy + + + blast_pq() + + + heat_tree_pq() + + + tax_datatable() + + + multitax_bar_pq() + + + treemap_pq() + + + Reproduce + + + write_pq() + + + read_pq() + + + list_fastq_files() + + + track_wkflow() + + + track_wkflow_samples() + + + MakeTreeSEFromPhyloseq() + + + 1 + + + as.MPSE() + + + 3 + + + MakePhyloseqFromTreeSE() + + + 1 + + + as.phyloseq() + + + 3 + + + mp_plot_rarecurve() + + + 3 + + + Transform + + + See also table 2 + + + EstimateDiversity() + + + 1 + + + mp_plot_alpha() + + + 3 + + + Alpha_diversity_graph() + + + 4 + + + mp_plot_venn() + + + 3 + + + dist_permanova() + + + 2 + + + Mp_adonis() + + + 3 + + + tsne_phyloseq() + + + 4 + + + PlotAbundance() + + + 1 + + + comp_barplot() + + + 2 + + + mp_plot_abundance() + + + 3 + + + Phylogeny_profile() + + + 4 + + + + Mp_diff_analysis() + + + 3 + + A + C + B + D + E + F + G + H + I + + + Fig.2 + + + + + + + + + + diff --git a/paper/tengeler_MiscMetabar.svg b/paper/tengeler_MiscMetabar.svg new file mode 100644 index 00000000..dbc07d33 --- /dev/null +++ b/paper/tengeler_MiscMetabar.svg @@ -0,0 +1,12387 @@ + +151 taxa 485 932 sequences 1 534 occurences6 taxonomic levels4 variables 27 samplesSequences length: No refseq slot@otu_table@tax_table@sam_data@refseqTaxa(OTUs, ASVs, ...)SamplesMin nb seq per sample (A291772Nb samples with less than 500 seq : 0Min nb seq per taxa: 173 (1 ASV)Min seq length: No refseq slotMax nb seq 1 taxa in 1 sample: 17722Max nb of sample for one taxa (1726472): 27Nb of taxa present in 1 sample only: 0ADHDControl304050607080Richness (Hill 0)patient_status1020Shannon (Hill 1)4812Simpson (Hill 2)Hill Number 0 Control-ADHDHill Number 1 Control-ADHDHill Number 2 Control-ADHD-10-50510Differences in mean levels (value and confidence intervals at 95%)Tuckey HSD testing for differences in mean Hill numbers531141745312631121341434212111102040Intersection size050100Set sizeControl_Cohort_1ADHD_Cohort_3Control_Cohort_3ADHD_Cohort_2Control_Cohort_2ADHD_Cohort_1patient_status_vs_cohortBacteriaFirmicutesVerrucomicrobiaBacteroidetesProteobacteriaCyanobacteriaClostridiaErysipelotrichiaVerrucomicrobiaeBacteroidiaGammaproteobacteriaMelainabacteriaClostridialesErysipelotrichalesVerrucomicrobialesBacteroidalesOceanospirillalesEnterobacterialesGastranaerophilalesRuminococcaceaeErysipelotrichaceaeLachnospiraceaeVerrucomicrobiaceaeClostridiaceae_1PorphyromonadaceaeBacteroidales_S24-7_groupBacteroidaceaePrevotellaceaeRikenellaceaeHalomonadaceaeEnterobacteriaceaeChristensenellaceaeEubacteriaceae[Eubacterium]_coprostanoligenes_group[Clostridium]_innocuum_groupDielmaEpulopisciumHoldemaniaAkkermansiaErysipelatoclostridiumClostridium_sensu_stricto_1Parabacteroidesuncultured_bacteriumunculturedCoprobacterBacteroidesParaprevotellaBarnesiellaOdoribacterAlistipesHalomonasEscherichia-ShigellaCoprococcus_2FusicatenibacterLachnoclostridium[Ruminococcus]_gnavus_groupHungatellaunculturedEisenbergiella[Eubacterium]_rectale_group[Ruminococcus]_gauvreauii_groupRoseburiaAnaerostipes[Eubacterium]_xylanophilum_group[Eubacterium]_fissicatena_groupCatabacterLachnospiraceae_ND3007_groupRuminococcaceae_UCG-014ButyricicoccusRuminococcaceae_UCG-004unculturedFlavonifractorRuminiclostridium_9AnaerotruncusRuminococcus_2FaecalibacteriumRuminococcus_1SubdoligranulumRuminiclostridium_5Ruminococcaceae_UCG-013EubacteriumBlautia 1.0 14.0 30.4 51.1 77.1110.0151.0 182 16200 58300126000220000340000486000..2..1NodesCohort_1 (10 sam.)Cohort_2 (10 sam.)Cohort_3 (7 sam.)0(0%)0(0%)0(0%)24(16%)2(1%)8(5%)117(77%)-20-100102030BacteroidesFaecalibacteriumParaprevotellaHungatellaRuminococcaceae_UCG-013Ruminococcaceae_UCG-014ParabacteroidesunculturedCatabacter[Ruminococcus]_gauvreauii_groupBlautiataxlog2FoldChangecol_taxBacteroidetesFirmicutesChange in abundance for patient_status (top:ADHD vs down:Control)ADHDControlBacteroidetesCyanobacteriaFirmicutesProteobacteriaVerrucomicrobiaBacteroidiaMelainabacteriaClostridiaErysipelotrichiaGammaproteobacteriaVerrucomicrobiae012345012345BacteroidalesGastranaerophilalesClostridialesErysipelotrichalesEnterobacterialesOceanospirillalesVerrucomicrobialesAbundanceLVL3Control (14 samples)Control (14 samples)ADHD (13 samples)ADHD (13 samples)6625255741276002356822263199871707614726129481034681787192560250404534447142964229387938753743364433623226318731443116304530402693265524872466239223072230195218631732169616631626130711701079107910689388607466465334341726471517264791726472131726471321726471817264740172647221726476117264714517264781726471901726471917264734172647166172647167172647531726471891726472917264748172647271726472517264747172647241726472172647261726473117264711726470Samples-5.0-2.50.02.55.0Abstats::reorder(OTU, Abundance)modalityADHDControl0255075010000200003000040000Number of sequencesNumber of OTUs (with standard error)factA110A111A12A13A14A15A16A17A18A19A21A210A22A23A24A25A26A27A28A29A33A34A35A36A37A38A39ABCDEFGHI From 9e397fa4b01ccf1dee8b1e8c5d576ca79d0506fb Mon Sep 17 00:00:00 2001 From: Adrien Taudiere <6680165+adrientaudiere@users.noreply.github.com> Date: Wed, 6 Dec 2023 16:03:45 +0100 Subject: [PATCH 4/9] Update figure --- paper/figures_svg/table1_publication.svg | 1570 ++++++++++++++++++++++ 1 file changed, 1570 insertions(+) create mode 100644 paper/figures_svg/table1_publication.svg diff --git a/paper/figures_svg/table1_publication.svg b/paper/figures_svg/table1_publication.svg new file mode 100644 index 00000000..6da525dc --- /dev/null +++ b/paper/figures_svg/table1_publication.svg @@ -0,0 +1,1570 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MiscMetabar + + + Other packages + + + 1. Mia — 2. microViz — 3.MicrobiotaProcess — 4. Phylosmith + + + Conversion to physeq + + + Conversion from physeq + + + Describe + + + summary_plot_pq() + + + krona() + + + sankey_pq() + + + accu_plot() + + + SRS_curve_pq() + + + clean_pq() + + + filter_asv_blast() + + + asv2otu() + + + lulu_pq() + + + E + x + p + l + o + r + e + + + Alpha-diversity + + + hill_pq() + + + Beta-diversity + + + ggvenn_pq() + + + upset_pq() + + + graph_test_pq() + + + adonis_pq() + + + plot_tsne_pq() + + + plot_tax_pq() + + + circle_pq() + + + amplicon::tax_circlize() + + + Compare 2 modalities + + + biplot_pq() + + + compare_pairs_pq() + + + Differential abundance + + + plot_deseq2_pq() + + + Taxonomy + + + blast_pq() + + + heat_tree_pq() + + + tax_datatable() + + + multitax_bar_pq() + + + treemap_pq() + + + Reproduce + + + write_pq() + + + read_pq() + + + list_fastq_files() + + + track_wkflow() + + + track_wkflow_samples() + + + MakeTreeSEFromPhyloseq() + + + 1 + + + as.MPSE() + + + 3 + + + MakePhyloseqFromTreeSE() + + + 1 + + + as.phyloseq() + + + 3 + + + mp_plot_rarecurve() + + + 3 + + + Transform + + + See also table 2 + + + EstimateDiversity() + + + 1 + + + mp_plot_alpha() + + + 3 + + + Alpha_diversity_graph() + + + 4 + + + mp_plot_venn() + + + 3 + + + dist_permanova() + + + 2 + + + Mp_adonis() + + + 3 + + + tsne_phyloseq() + + + 4 + + + PlotAbundance() + + + 1 + + + comp_barplot() + + + 2 + + + mp_plot_abundance() + + + 3 + + + Phylogeny_profile() + + + 4 + + + + Mp_diff_analysis() + + + 3 + + A + C + B + D + E + F + G + H + I + + + Fig.2 + + + + + + + + + + From bbaf87efb14ac84ca7a5b33e2280685092539bae Mon Sep 17 00:00:00 2001 From: Adrien Taudiere <6680165+adrientaudiere@users.noreply.github.com> Date: Wed, 6 Dec 2023 16:28:53 +0100 Subject: [PATCH 5/9] Update installation script --- README.md | 26 ++++++++++++++++++++++---- 1 file changed, 22 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 0d024141..590d0439 100644 --- a/README.md +++ b/README.md @@ -36,14 +36,24 @@ heavily on the R packages ## Installation -There is no CRAN or bioconductor version of MiscMetabar for now (work in -progress). +There is no CRAN version of MiscMetabar for now (work in +progress). As MiscMetabar heavily relies on two bioconductor packages +(dada and phyloseq), we need to first install those 2 packages using +BiocManager. You can install the stable version from [GitHub](https://github.com/) with: ``` r -install.packages("devtools") +if (!require("BiocManager", quietly = TRUE)){ + install.packages("BiocManager") +} +BiocManager::install("dada2") +BiocManager::install("phyloseq") + +if (!require("devtools", quietly = TRUE)){ + install.packages("devtools") +} devtools::install_github("adrientaudiere/MiscMetabar") ``` @@ -51,7 +61,15 @@ You can install the developement version from [GitHub](https://github.com/) with: ``` r -install.packages("devtools") +if (!require("BiocManager", quietly = TRUE)) { + install.packages("BiocManager") +} +BiocManager::install("dada2") +BiocManager::install("phyloseq") + +if (!require("devtools", quietly = TRUE)){ + install.packages("devtools") +} devtools::install_github("adrientaudiere/MiscMetabar", ref = "dev") ``` From 5aa501ffaeb65724e09e266ada6d66d9bba9a97a Mon Sep 17 00:00:00 2001 From: Adrien Taudiere <6680165+adrientaudiere@users.noreply.github.com> Date: Wed, 6 Dec 2023 16:30:09 +0100 Subject: [PATCH 6/9] Update README.md --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 590d0439..3ffd9e26 100644 --- a/README.md +++ b/README.md @@ -125,6 +125,9 @@ Result of the Tuckey post-hoc test ### Beta-diversity analysis ``` r +if (!require("ggVennDiagram", quietly = TRUE)){ + install.packages("ggVennDiagram") +} ggvenn_pq(data_fungi, fact = "Height") + ggplot2::scale_fill_distiller(palette = "BuPu", direction = 1) + labs(title = "Share number of ASV among Height in tree") From 22a1c600b3fda28b3627e0218ebebb279fa3922c Mon Sep 17 00:00:00 2001 From: Markus Ankenbrand Date: Fri, 8 Dec 2023 08:53:51 +0100 Subject: [PATCH 7/9] Add remotes for bioc packages --- DESCRIPTION | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ac855779..af32e82e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -80,7 +80,9 @@ Remotes: github::mikemc/speedyseq, github::adrientaudiere/lulu, github::david-barnett/microViz, - github::erocoar/gghalves + github::erocoar/gghalves, + bioc::release/phyloseq, + bioc::release/dada2 Config/testthat/edition: 3 Config/testthat/parallel: true VignetteBuilder: knitr From d599627b48d7b29573661deebf788352e6a2970f Mon Sep 17 00:00:00 2001 From: Adrien Taudiere <6680165+adrientaudiere@users.noreply.github.com> Date: Fri, 8 Dec 2023 14:07:17 +0100 Subject: [PATCH 8/9] Update DESCRIPTION --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index af32e82e..fe720c4a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -81,8 +81,8 @@ Remotes: github::adrientaudiere/lulu, github::david-barnett/microViz, github::erocoar/gghalves, - bioc::release/phyloseq, - bioc::release/dada2 + bioc::phyloseq, + bioc::dada2 Config/testthat/edition: 3 Config/testthat/parallel: true VignetteBuilder: knitr From 5dc201543b48c654844a2bd3185170ca2a5b27b6 Mon Sep 17 00:00:00 2001 From: Adrien Taudiere <6680165+adrientaudiere@users.noreply.github.com> Date: Mon, 11 Dec 2023 16:14:10 +0100 Subject: [PATCH 9/9] Update DESCRIPTION --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 03dd981b..2ca939c2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -95,8 +95,8 @@ Remotes: github::adrientaudiere/lulu, github::david-barnett/microViz, github::erocoar/gghalves, - bioc::release/phyloseq, - bioc::release/dada2, + bioc::phyloseq, + bioc::dada2, github::brendanf/FUNGuildR Config/testthat/edition: 3 Config/testthat/parallel: true