MaAsLin2 User Manual

MaAsLin2 is the next generation of MaAsLin (Microbiome Multivariable Association with Linear Models).

MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta-omics features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, along with a variety of filtering, normalization, and transform methods.

If you use the MaAsLin2 software, please cite our manuscript:

Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C (2021). Multivariable Association Discovery in Population-scale Meta-omics Studies. PLoS Computational Biology, 17(11):e1009442.

Check out the MaAsLin 2 tutorial for an overview of analysis options.

If you have questions, please direct it to :
MaAsLin2 Forum
Google Groups (Read only)


Description

MaAsLin2 finds associations between microbiome multi-omics features and complex metadata in population-scale epidemiological studies. The software includes multiple analysis methods (with support for multiple covariates and repeated measures), filtering, normalization, and transform options to customize analysis for your specific study.

Requirements

MaAsLin2 is an R package that can be run on the command line or as an R function.

Installation

MaAsLin2 can be run from the command line or as an R function. If only running from the command line, you do not need to install the MaAsLin2 package but you will need to install the MaAsLin2 dependencies.

From command line

  1. Download the source: MaAsLin2.tar.gz
  2. Decompress the download:
    • $ tar xzvf maaslin2.tar.gz
  3. Install the Bioconductor dependencies edgeR and metagenomeSeq.
  4. Install the CRAN dependencies:
    • $ R -q -e "install.packages(c('lmerTest','pbapply','car','dplyr','vegan','chemometrics','ggplot2','pheatmap','hash','logging','data.table','glmmTMB','MASS','cplm','pscl'), repos='http://cran.r-project.org')"
  5. Install the MaAsLin2 package (only r,equired if running as an R function):
    • $ R CMD INSTALL maaslin2

From R

Install Bioconductor and then install Maaslin2

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Maaslin2")

How to Run

MaAsLin2 can be run from the command line or as an R function. Both methods require the same arguments, have the same options, and use the same default settings.

Input Files

MaAsLin2 requires two input files.

  1. Data (or features) file
    • This file is tab-delimited.
    • Formatted with features as columns and samples as rows.
    • The transpose of this format is also okay.
    • Possible features in this file include taxonomy or genes.
  2. Metadata file
    • This file is tab-delimited.
    • Formatted with features as columns and samples as rows.
    • The transpose of this format is also okay.
    • Possible metadata in this file include gender or age.

The data file can contain samples not included in the metadata file (along with the reverse case). For both cases, those samples not included in both files will be removed from the analysis. Also the samples do not need to be in the same order in the two files.

NOTE: If running MaAsLin2 as a function, the data and metadata inputs can be of type data.frame instead of a path to a file.

Output Files

MaAsLin2 generates two types of output files: data and visualization.

  1. Data output files
    • all_results.tsv
      • This includes the same data as the data.frame returned.
      • This file contains all results ordered by increasing q-value.
      • The first columns are the metadata and feature names.
      • The next two columns are the value and coefficient from the model.
      • The next column is the standard deviation from the model.
      • The N column is the total number of data points.
      • The N.not.zero column is the total of non-zero data points.
      • The pvalue from the calculation is the second to last column.
      • The qvalue is computed with p.adjust with the correction method.
    • significant_results.tsv
      • This file is a subset of the results in the first file.
      • It only includes associations with q-values <= to the threshold.
    • ``features```
      • This folder includes the filtered, normalized, and transformed versions of the input feature table.
      • These steps are performed sequentially in the above order.
      • If an option is set such that a step does not change the data, the resulting table will still be output.
    • models.rds
      • This file contains a list with every model fit object.
      • It will only be generated if save_models is set to TRUE.
    • residuals.rds
      • This file contains a data frame with residuals for each feature.
    • fitted.rds
      • This file contains a data frame with fitted values for each feature.
    • ranef.rds
      • This file contains a data frame with extracted random effects for each feature (when random effects are specified).
    • maaslin2.log
      • This file contains all log information for the run.
      • It includes all settings, warnings, errors, and steps run.
  2. Visualization output files
    • heatmap.pdf
      • This file contains a heatmap of the significant associations.
    • [a-z/0-9]+.pdf
      • A plot is generated for each significant association.
      • Scatter plots are used for continuous metadata.
      • Box plots are for categorical data.
      • Data points plotted are after filtering but prior to normalization and transform.

Run a Demo

Example input files can be found in the inst/extdata folder of the MaAsLin2 source. The files provided were generated from the HMP2 data which can be downloaded from https://ibdmdb.org/ .

HMP2_taxonomy.tsv: is a tab-demilited file with species as columns and samples as rows. It is a subset of the taxonomy file so it just includes the species abundances for all samples.

HMP2_metadata.tsv: is a tab-delimited file with samples as rows and metadata as columns. It is a subset of the metadata file so that it just includes some of the fields.

Command line

$ Maaslin2.R --fixed_effects="diagnosis,dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age" --random_effects="site,subject" --standardize=FALSE inst/extdata/HMP2_taxonomy.tsv inst/extdata/HMP2_metadata.tsv demo_output

  • Make sure to provide the full path to the MaAsLin2 executable (ie ./R/Maaslin2.R).
  • In the demo command:
    • HMP2_taxonomy.tsv is the path to your data (or features) file
    • HMP2_metadata.tsv is the path to your metadata file
    • demo_output is the path to the folder to write the output

In R

library(Maaslin2)
input_data <- system.file(
    'extdata','HMP2_taxonomy.tsv', package="Maaslin2")
input_metadata <-system.file(
    'extdata','HMP2_metadata.tsv', package="Maaslin2")
fit_data <- Maaslin2(
    input_data, input_metadata, 'demo_output',
    fixed_effects = c('diagnosis', 'dysbiosisnonIBD','dysbiosisUC','dysbiosisCD', 'antibiotics', 'age'),
    random_effects = c('site', 'subject'),
    reference = "diagnosis,nonIBD",
    standardize = FALSE)
## [1] "Creating output folder"
## [1] "Creating output feature tables folder"
## [1] "Creating output fits folder"
## [1] "Creating output figures folder"
## 2025-04-27 16:44:44.462502 INFO::Writing function arguments to log file
## 2025-04-27 16:44:44.472328 INFO::Verifying options selected are valid
## 2025-04-27 16:44:44.486601 INFO::Determining format of input files
## 2025-04-27 16:44:44.491745 INFO::Input format is data samples as rows and metadata samples as rows
## 2025-04-27 16:44:44.493927 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2025-04-27 16:44:44.494334 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2025-04-27 16:44:44.495141 INFO::Filter data based on min abundance and min prevalence
## 2025-04-27 16:44:44.495387 INFO::Total samples in data: 1595
## 2025-04-27 16:44:44.495617 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2025-04-27 16:44:44.497722 INFO::Total filtered features: 0
## 2025-04-27 16:44:44.498053 INFO::Filtered feature names from abundance and prevalence filtering:
## 2025-04-27 16:44:44.501251 INFO::Total filtered features with variance filtering: 0
## 2025-04-27 16:44:44.50156 INFO::Filtered feature names from variance filtering:
## 2025-04-27 16:44:44.501788 INFO::Running selected normalization method: TSS
## 2025-04-27 16:44:44.966368 INFO::Bypass z-score application to metadata
## 2025-04-27 16:44:44.966973 INFO::Running selected transform method: LOG
## 2025-04-27 16:44:44.974188 INFO::Running selected analysis method: LM
## 2025-04-27 16:44:45.102557 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:45.268494 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2025-04-27 16:44:45.328332 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2025-04-27 16:44:45.419351 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:45.586116 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2025-04-27 16:44:45.64487 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:45.70029 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2025-04-27 16:44:45.754967 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2025-04-27 16:44:45.8198 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2025-04-27 16:44:45.873472 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2025-04-27 16:44:45.928636 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:45.99087 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:46.043972 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:46.100088 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2025-04-27 16:44:46.153526 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:46.209251 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2025-04-27 16:44:46.262673 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2025-04-27 16:44:46.316496 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## Feature Bacteroides.thetaiotaomicron : simpleWarning: Model failed to converge with 1 negative eigenvalue: -2.3e+00
## 2025-04-27 16:44:46.364717 WARNING::Fitting problem for feature 18 a warning was issued
## boundary (singular) fit: see help('isSingular')
## Warning: Model failed to converge with 1 negative eigenvalue: -2.3e+00
## 2025-04-27 16:44:46.415929 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:46.46718 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:46.52674 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:46.579352 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2025-04-27 16:44:46.633599 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2025-04-27 16:44:46.692697 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2025-04-27 16:44:46.746692 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2025-04-27 16:44:46.799785 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:46.855829 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2025-04-27 16:44:46.909488 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2025-04-27 16:44:46.965073 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:47.02333 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2025-04-27 16:44:47.078303 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2025-04-27 16:44:47.132116 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:47.19293 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:47.247533 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:47.307974 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:47.361391 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2025-04-27 16:44:47.416743 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2025-04-27 16:44:47.47278 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2025-04-27 16:44:47.528844 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:47.591198 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:47.645742 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:47.701565 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:47.753795 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2025-04-27 16:44:47.815436 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2025-04-27 16:44:47.867456 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:47.924281 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:47.978459 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2025-04-27 16:44:48.035488 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2025-04-27 16:44:48.092293 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:48.153173 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:48.212659 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:48.266711 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:48.336049 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:48.39603 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2025-04-27 16:44:48.447801 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2025-04-27 16:44:48.536311 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2025-04-27 16:44:48.59154 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:48.651715 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:48.721151 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:48.778524 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:48.835099 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2025-04-27 16:44:49.002799 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:49.057202 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:49.109717 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2025-04-27 16:44:49.173412 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2025-04-27 16:44:49.226744 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2025-04-27 16:44:49.279946 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:49.32942 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2025-04-27 16:44:49.385736 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2025-04-27 16:44:49.440481 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:49.495581 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2025-04-27 16:44:49.553448 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2025-04-27 16:44:49.609479 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:49.662309 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2025-04-27 16:44:49.720929 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:49.773212 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:49.823897 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2025-04-27 16:44:49.879035 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2025-04-27 16:44:49.931668 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2025-04-27 16:44:49.983463 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2025-04-27 16:44:50.043899 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2025-04-27 16:44:50.102188 INFO::Fitting model to feature number 82, Escherichia.coli
## 2025-04-27 16:44:50.156126 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2025-04-27 16:44:50.209315 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:50.259385 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2025-04-27 16:44:50.31694 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2025-04-27 16:44:50.370138 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2025-04-27 16:44:50.44292 INFO::Counting total values for each feature
## 2025-04-27 16:44:50.455825 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2025-04-27 16:44:50.503775 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2025-04-27 16:44:50.561883 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2025-04-27 16:44:50.642135 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2025-04-27 16:44:50.673822 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2025-04-27 16:44:50.690549 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2025-04-27 16:44:50.693638 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2025-04-27 16:44:50.696518 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): demo_output/significant_results.tsv
## 2025-04-27 16:44:50.697843 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2025-04-27 16:44:50.75379 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2025-04-27 16:44:50.756577 INFO::Plotting associations from most to least significant, grouped by metadata
## 2025-04-27 16:44:50.756977 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2025-04-27 16:44:50.757694 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2025-04-27 16:44:50.877029 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2025-04-27 16:44:50.982527 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2025-04-27 16:44:51.08402 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2025-04-27 16:44:51.173044 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2025-04-27 16:44:51.270027 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2025-04-27 16:44:51.36022 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2025-04-27 16:44:51.455426 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2025-04-27 16:44:51.545378 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2025-04-27 16:44:51.639183 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2025-04-27 16:44:51.729083 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2025-04-27 16:44:51.82496 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2025-04-27 16:44:51.91799 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2025-04-27 16:44:52.008414 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2025-04-27 16:44:52.121277 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2025-04-27 16:44:52.209176 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2025-04-27 16:44:52.308943 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2025-04-27 16:44:52.404148 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2025-04-27 16:44:52.500656 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2025-04-27 16:44:52.592626 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-27 16:44:52.69439 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2025-04-27 16:44:52.807444 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2025-04-27 16:44:52.89948 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2025-04-27 16:44:52.989504 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2025-04-27 16:44:53.08024 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2025-04-27 16:44:53.179988 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2025-04-27 16:44:53.274641 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2025-04-27 16:44:53.37562 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2025-04-27 16:44:53.465448 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2025-04-27 16:44:53.564429 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2025-04-27 16:44:53.65161 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2025-04-27 16:44:53.750875 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2025-04-27 16:44:53.839511 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2025-04-27 16:44:53.928872 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2025-04-27 16:44:54.018086 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2025-04-27 16:44:54.109296 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2025-04-27 16:44:54.203854 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2025-04-27 16:44:54.297186 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2025-04-27 16:44:54.396343 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2025-04-27 16:44:54.482913 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2025-04-27 16:44:54.575237 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2025-04-27 16:44:54.673107 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2025-04-27 16:44:54.766462 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2025-04-27 16:44:54.864555 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2025-04-27 16:44:54.953836 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2025-04-27 16:44:55.048312 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2025-04-27 16:44:55.134283 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2025-04-27 16:44:55.232881 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2025-04-27 16:44:55.339894 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2025-04-27 16:44:55.438955 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2025-04-27 16:44:55.533131 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2025-04-27 16:44:55.620379 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2025-04-27 16:44:55.718003 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2025-04-27 16:44:55.811905 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2025-04-27 16:44:55.897948 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2025-04-27 16:44:55.992346 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2025-04-27 16:44:56.078769 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2025-04-27 16:44:56.168786 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2025-04-27 16:44:56.305885 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2025-04-27 16:44:56.40005 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2025-04-27 16:44:56.502597 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2025-04-27 16:44:56.591119 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2025-04-27 16:44:56.683443 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2025-04-27 16:44:57.665915 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2025-04-27 16:44:57.666922 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2025-04-27 16:44:57.749669 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2025-04-27 16:44:57.839379 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2025-04-27 16:44:57.940729 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2025-04-27 16:44:58.038017 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2025-04-27 16:44:58.145574 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2025-04-27 16:44:58.243885 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2025-04-27 16:44:58.355129 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2025-04-27 16:44:58.457814 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2025-04-27 16:44:58.555024 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2025-04-27 16:44:58.652934 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2025-04-27 16:44:58.745066 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2025-04-27 16:44:58.850007 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-27 16:44:58.944322 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2025-04-27 16:44:59.054438 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2025-04-27 16:44:59.154712 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2025-04-27 16:44:59.253367 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2025-04-27 16:44:59.353798 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2025-04-27 16:44:59.44505 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2025-04-27 16:44:59.5453 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2025-04-27 16:44:59.640934 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2025-04-27 16:44:59.734629 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2025-04-27 16:44:59.83255 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2025-04-27 16:44:59.924536 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2025-04-27 16:45:00.031588 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2025-04-27 16:45:00.165966 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2025-04-27 16:45:00.265078 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2025-04-27 16:45:00.3653 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2025-04-27 16:45:00.451757 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2025-04-27 16:45:00.548579 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2025-04-27 16:45:00.642794 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2025-04-27 16:45:00.740415 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2025-04-27 16:45:00.84118 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2025-04-27 16:45:00.946046 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2025-04-27 16:45:01.044895 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2025-04-27 16:45:01.150995 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2025-04-27 16:45:01.256608 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2025-04-27 16:45:01.351607 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2025-04-27 16:45:01.458138 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2025-04-27 16:45:01.5584 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2025-04-27 16:45:01.663784 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2025-04-27 16:45:01.756212 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2025-04-27 16:45:01.864182 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2025-04-27 16:45:01.962761 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2025-04-27 16:45:02.928113 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2025-04-27 16:45:02.92906 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2025-04-27 16:45:03.014944 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2025-04-27 16:45:03.118027 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2025-04-27 16:45:03.218132 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2025-04-27 16:45:03.32487 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2025-04-27 16:45:03.417394 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-27 16:45:03.52284 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2025-04-27 16:45:03.623326 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2025-04-27 16:45:03.719328 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2025-04-27 16:45:03.986412 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2025-04-27 16:45:04.070223 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2025-04-27 16:45:04.161282 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2025-04-27 16:45:04.250611 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2025-04-27 16:45:04.344282 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2025-04-27 16:45:04.432816 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2025-04-27 16:45:04.525741 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2025-04-27 16:45:04.610214 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2025-04-27 16:45:04.699199 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2025-04-27 16:45:04.794547 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2025-04-27 16:45:04.878305 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2025-04-27 16:45:04.967314 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2025-04-27 16:45:05.05349 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2025-04-27 16:45:05.148238 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2025-04-27 16:45:05.236271 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2025-04-27 16:45:05.329487 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2025-04-27 16:45:05.419964 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2025-04-27 16:45:05.517487 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2025-04-27 16:45:05.609957 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2025-04-27 16:45:05.700031 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2025-04-27 16:45:06.624584 INFO::Plotting data for metadata number 4, antibiotics
## 2025-04-27 16:45:06.625523 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2025-04-27 16:45:06.690492 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2025-04-27 16:45:06.779195 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2025-04-27 16:45:06.861998 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2025-04-27 16:45:06.953412 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2025-04-27 16:45:07.036136 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2025-04-27 16:45:07.124667 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2025-04-27 16:45:07.207715 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2025-04-27 16:45:07.291303 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2025-04-27 16:45:07.423373 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2025-04-27 16:45:07.51491 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2025-04-27 16:45:07.617061 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2025-04-27 16:45:07.699742 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2025-04-27 16:45:07.793715 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2025-04-27 16:45:07.878464 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2025-04-27 16:45:07.971935 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-27 16:45:08.058708 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2025-04-27 16:45:08.149402 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2025-04-27 16:45:08.23009 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2025-04-27 16:45:08.319135 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2025-04-27 16:45:08.451462 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2025-04-27 16:45:08.539583 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2025-04-27 16:45:08.619189 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2025-04-27 16:45:08.711646 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2025-04-27 16:45:08.798911 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2025-04-27 16:45:08.893159 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2025-04-27 16:45:08.974679 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2025-04-27 16:45:09.071307 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2025-04-27 16:45:09.163743 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2025-04-27 16:45:09.263057 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2025-04-27 16:45:09.350044 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2025-04-27 16:45:09.441901 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2025-04-27 16:45:09.524488 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2025-04-27 16:45:09.614796 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2025-04-27 16:45:09.707325 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2025-04-27 16:45:09.790705 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2025-04-27 16:45:09.877145 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2025-04-27 16:45:09.953421 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2025-04-27 16:45:10.035703 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2025-04-27 16:45:10.112736 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2025-04-27 16:45:11.047238 INFO::Plotting data for metadata number 5, age
## 2025-04-27 16:45:11.048092 INFO::Creating scatter plot for continuous data, age vs Haemophilus.parainfluenzae
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:11.14088 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.pseudocatenulatum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:11.274381 INFO::Creating scatter plot for continuous data, age vs Faecalibacterium.prausnitzii
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:11.36869 INFO::Creating scatter plot for continuous data, age vs Clostridium.clostridioforme
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:11.467447 INFO::Creating scatter plot for continuous data, age vs Veillonella.parvula
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:11.5645 INFO::Creating scatter plot for continuous data, age vs Subdoligranulum.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:11.663898 INFO::Creating scatter plot for continuous data, age vs Clostridium.symbiosum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:11.755958 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.gnavus
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:11.856823 INFO::Creating scatter plot for continuous data, age vs Dialister.invisus
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:11.949368 INFO::Creating scatter plot for continuous data, age vs Veillonella.dispar
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:12.03943 INFO::Creating scatter plot for continuous data, age vs Veillonella.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:12.140463 INFO::Creating scatter plot for continuous data, age vs Bacteroides.thetaiotaomicron
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:12.221201 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.bromii
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:12.318477 INFO::Creating scatter plot for continuous data, age vs Bacteroides.intestinalis
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:12.414917 INFO::Creating scatter plot for continuous data, age vs Eubacterium.siraeum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:12.498228 INFO::Creating scatter plot for continuous data, age vs Prevotella.copri
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:12.602753 INFO::Creating scatter plot for continuous data, age vs Alistipes.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:12.697817 INFO::Creating scatter plot for continuous data, age vs Bacteroidales.bacterium.ph8
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:12.779946 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.longum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:12.873977 INFO::Creating scatter plot for continuous data, age vs Akkermansia.muciniphila
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:12.973505 INFO::Creating scatter plot for continuous data, age vs Collinsella.aerofaciens
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:13.059863 INFO::Creating scatter plot for continuous data, age vs Parabacteroides.distasonis
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-27 16:45:14.140696 INFO::Plotting data for metadata number 6, diagnosis
## 2025-04-27 16:45:14.141613 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2025-04-27 16:45:14.216848 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2025-04-27 16:45:14.36892 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2025-04-27 16:45:14.470488 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2025-04-27 16:45:14.57782 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2025-04-27 16:45:14.681719 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2025-04-27 16:45:14.777487 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2025-04-27 16:45:14.879614 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2025-04-27 16:45:14.968897 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2025-04-27 16:45:15.06759 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2025-04-27 16:45:15.159442 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2025-04-27 16:45:15.255196 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2025-04-27 16:45:15.352297 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2025-04-27 16:45:15.437304 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2025-04-27 16:45:15.530176 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2025-04-27 16:45:15.618397 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2025-04-27 16:45:15.713492 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2025-04-27 16:45:15.80326 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2025-04-27 16:45:15.904852 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2025-04-27 16:45:16.005994 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2025-04-27 16:45:16.093099 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2025-04-27 16:45:16.193713 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2025-04-27 16:45:16.287022 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2025-04-27 16:45:16.390861 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2025-04-27 16:45:16.489239 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2025-04-27 16:45:16.577951 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2025-04-27 16:45:16.6814 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2025-04-27 16:45:16.780093 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2025-04-27 16:45:16.879787 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2025-04-27 16:45:16.985423 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2025-04-27 16:45:17.081248 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2025-04-27 16:45:17.184648 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2025-04-27 16:45:17.286111 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2025-04-27 16:45:17.383104 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2025-04-27 16:45:17.493316 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2025-04-27 16:45:17.597466 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2025-04-27 16:45:17.701691 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2025-04-27 16:45:17.848432 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2025-04-27 16:45:17.947996 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2025-04-27 16:45:18.060233 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2025-04-27 16:45:18.179755 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2025-04-27 16:45:18.28027 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2025-04-27 16:45:18.380536 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.siraeum
Session Info

Session info from running the demo in R can be displayed with the following command.

sessionInfo()
## R version 4.5.0 Patched (2025-04-21 r88169)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] Maaslin2_1.23.0
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6        biglm_0.9-3         xfun_0.52          
##  [4] bslib_0.9.0         ggplot2_3.5.2       lattice_0.22-7     
##  [7] numDeriv_2016.8-1.1 vctrs_0.6.5         tools_4.5.0        
## [10] Rdpack_2.6.4        generics_0.1.3      parallel_4.5.0     
## [13] getopt_1.20.4       tibble_3.2.1        DEoptimR_1.1-3-1   
## [16] cluster_2.1.8.1     pkgconfig_2.0.3     logging_0.10-108   
## [19] pheatmap_1.0.12     Matrix_1.7-3        data.table_1.17.0  
## [22] RColorBrewer_1.1-3  lifecycle_1.0.4     compiler_4.5.0     
## [25] farver_2.1.2        lmerTest_3.1-3      permute_0.9-7      
## [28] htmltools_0.5.8.1   sass_0.4.10         hash_2.2.6.3       
## [31] yaml_2.3.10         pillar_1.10.2       nloptr_2.2.1       
## [34] crayon_1.5.3        jquerylib_0.1.4     MASS_7.3-65        
## [37] cachem_1.1.0        vegan_2.6-10        reformulas_0.4.0   
## [40] boot_1.3-31         nlme_3.1-168        robustbase_0.99-4-1
## [43] tidyselect_1.2.1    digest_0.6.37       mvtnorm_1.3-3      
## [46] dplyr_1.1.4         labeling_0.4.3      splines_4.5.0      
## [49] pcaPP_2.0-5         fastmap_1.2.0       grid_4.5.0         
## [52] cli_3.6.5           magrittr_2.0.3      dichromat_2.0-0.1  
## [55] withr_3.0.2         scales_1.4.0        rmarkdown_2.29     
## [58] lme4_1.1-37         pbapply_1.7-2       evaluate_1.0.3     
## [61] knitr_1.50          rbibutils_2.3       mgcv_1.9-3         
## [64] rlang_1.1.6         Rcpp_1.0.14         glue_1.8.0         
## [67] optparse_1.7.5      DBI_1.2.3           minqa_1.2.8        
## [70] jsonlite_2.0.0      R6_2.6.1

Options

Run MaAsLin2 help to print a list of the options and the default settings.

$ Maaslin2.R –help Usage: ./R/Maaslin2.R options <data.tsv> <metadata.tsv>

Options: -h, –help Show this help message and exit

-a MIN_ABUNDANCE, --min_abundance=MIN_ABUNDANCE
    The minimum abundance for each feature [ Default: 0 ]

-p MIN_PREVALENCE, --min_prevalence=MIN_PREVALENCE
    The minimum percent of samples for which a feature 
    is detected at minimum abundance [ Default: 0.1 ]

-b MIN_VARIANCE, --min_variance=MIN_VARIANCE
    Keep features with variance greater than [ Default: 0.0 ]

-s MAX_SIGNIFICANCE, --max_significance=MAX_SIGNIFICANCE
    The q-value threshold for significance [ Default: 0.25 ]

-n NORMALIZATION, --normalization=NORMALIZATION
    The normalization method to apply [ Default: TSS ]
    [ Choices: TSS, CLR, CSS, NONE, TMM ]

-t TRANSFORM, --transform=TRANSFORM
    The transform to apply [ Default: LOG ]
    [ Choices: LOG, LOGIT, AST, NONE ]

-m ANALYSIS_METHOD, --analysis_method=ANALYSIS_METHOD
    The analysis method to apply [ Default: LM ]
    [ Choices: LM, CPLM, NEGBIN, ZINB ]

-r RANDOM_EFFECTS, --random_effects=RANDOM_EFFECTS
    The random effects for the model, comma-delimited
    for multiple effects [ Default: none ]

-f FIXED_EFFECTS, --fixed_effects=FIXED_EFFECTS
    The fixed effects for the model, comma-delimited
    for multiple effects [ Default: all ]

-c CORRECTION, --correction=CORRECTION
    The correction method for computing the 
    q-value [ Default: BH ]

-z STANDARDIZE, --standardize=STANDARDIZE
    Apply z-score so continuous metadata are 
    on the same scale [ Default: TRUE ]

-l PLOT_HEATMAP, --plot_heatmap=PLOT_HEATMAP
    Generate a heatmap for the significant 
    associations [ Default: TRUE ]

-i HEATMAP_FIRST_N, --heatmap_first_n=HEATMAP_FIRST_N
    In heatmap, plot top N features with significant 
    associations [ Default: TRUE ]

-o PLOT_SCATTER, --plot_scatter=PLOT_SCATTER
    Generate scatter plots for the significant
    associations [ Default: TRUE ]
    
-g MAX_PNGS, --max_pngs=MAX_PNGS
    The maximum number of scatter plots for signficant associations 
    to save as png files [ Default: 10 ]

-O SAVE_SCATTER, --save_scatter=SAVE_SCATTER
    Save all scatter plot ggplot objects
    to an RData file [ Default: FALSE ]

-e CORES, --cores=CORES
    The number of R processes to run in parallel
    [ Default: 1 ]
    
-j SAVE_MODELS --save_models=SAVE_MODELS
    Return the full model outputs and save to an RData file
    [ Default: FALSE ]

-d REFERENCE, --reference=REFERENCE
    The factor to use as a reference level for a categorical variable 
    provided as a string of 'variable,reference', semi-colon delimited for 
    multiple variables. Not required if metadata is passed as a factor or 
    for variables with less than two levels but can be set regardless.
    [ Default: NA ] 

Troubleshooting

  1. Question: When I run from the command line I see the error Maaslin2.R: command not found. How do I fix this?
    • Answer: Provide the full path to the executable when running Maaslin2.R.
  2. Question: When I run as a function I see the error Error in library(Maaslin2): there is no package called 'Maaslin2'. How do I fix this?
    • Answer: Install the R package and then try loading the library again.
  3. Question: When I try to install the R package I see errors about dependencies not being installed. Why is this?
    • Answer: Installing the R package will not automatically install the packages MaAsLin2 requires. Please install the dependencies and then install the MaAsLin2 R package.