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"
## 2025-04-15 19:25:26.262274 INFO::Writing function arguments to log file
## 2025-04-15 19:25:26.294614 INFO::Verifying options selected are valid
## 2025-04-15 19:25:26.326716 INFO::Determining format of input files
## 2025-04-15 19:25:26.327954 INFO::Input format is data samples as rows and metadata samples as rows
## 2025-04-15 19:25:26.33234 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2025-04-15 19:25:26.333395 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2025-04-15 19:25:26.335503 INFO::Filter data based on min abundance and min prevalence
## 2025-04-15 19:25:26.336189 INFO::Total samples in data: 1595
## 2025-04-15 19:25:26.336821 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2025-04-15 19:25:26.341439 INFO::Total filtered features: 0
## 2025-04-15 19:25:26.3423 INFO::Filtered feature names from abundance and prevalence filtering:
## 2025-04-15 19:25:26.350756 INFO::Total filtered features with variance filtering: 0
## 2025-04-15 19:25:26.351646 INFO::Filtered feature names from variance filtering:
## 2025-04-15 19:25:26.352342 INFO::Running selected normalization method: TSS
## 2025-04-15 19:25:27.436001 INFO::Bypass z-score application to metadata
## 2025-04-15 19:25:27.437151 INFO::Running selected transform method: LOG
## 2025-04-15 19:25:27.452387 INFO::Running selected analysis method: LM
## 2025-04-15 19:25:27.779471 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:28.407038 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2025-04-15 19:25:28.55391 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2025-04-15 19:25:28.711356 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:28.867492 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2025-04-15 19:25:29.042312 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:29.184998 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2025-04-15 19:25:29.323843 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2025-04-15 19:25:29.474323 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2025-04-15 19:25:29.621771 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2025-04-15 19:25:29.771248 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
## boundary (singular) fit: see help('isSingular')
## Feature Bacteroides.finegoldii : simpleWarning: Model failed to converge with 1 negative eigenvalue: -7.9e+01
## 2025-04-15 19:25:29.898228 WARNING::Fitting problem for feature 11 a warning was issued
## boundary (singular) fit: see help('isSingular')
## Warning: Model failed to converge with 1 negative eigenvalue: -7.9e+01
## 2025-04-15 19:25:30.048308 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:30.185882 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:30.330158 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2025-04-15 19:25:30.473432 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:30.607982 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2025-04-15 19:25:30.75162 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2025-04-15 19:25:30.893582 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:31.036791 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:31.189196 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:31.336075 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:31.499004 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2025-04-15 19:25:31.64939 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2025-04-15 19:25:31.79359 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2025-04-15 19:25:31.948535 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2025-04-15 19:25:32.091359 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:32.234061 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2025-04-15 19:25:32.383618 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2025-04-15 19:25:32.529674 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:32.672991 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2025-04-15 19:25:32.82531 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2025-04-15 19:25:32.967161 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:33.107977 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:33.252885 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:33.403596 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:33.568763 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2025-04-15 19:25:33.713574 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2025-04-15 19:25:33.85019 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2025-04-15 19:25:34.000978 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:34.151536 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## Feature Clostridium.citroniae : simpleWarning: Model failed to converge with 1 negative eigenvalue: -3.4e+01
## 2025-04-15 19:25:34.275088 WARNING::Fitting problem for feature 40 a warning was issued
## boundary (singular) fit: see help('isSingular')
## Warning: Model failed to converge with 1 negative eigenvalue: -3.4e+01
## 2025-04-15 19:25:34.418683 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:34.55749 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:34.706544 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2025-04-15 19:25:34.860237 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2025-04-15 19:25:35.00255 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:35.142352 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:35.289997 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2025-04-15 19:25:35.43058 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2025-04-15 19:25:35.583682 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:35.73265 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:35.876315 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:36.017847 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:36.200188 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:36.355032 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2025-04-15 19:25:36.497733 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2025-04-15 19:25:36.881667 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2025-04-15 19:25:37.021772 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:37.1638 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:37.316028 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:37.461384 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:37.607515 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2025-04-15 19:25:37.74686 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:37.890074 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:38.029019 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2025-04-15 19:25:38.176513 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2025-04-15 19:25:38.321762 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2025-04-15 19:25:38.465003 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:38.603214 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2025-04-15 19:25:38.985485 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2025-04-15 19:25:39.134478 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:39.280228 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2025-04-15 19:25:39.426189 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2025-04-15 19:25:39.572948 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:39.712942 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2025-04-15 19:25:40.073883 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:40.216433 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:40.351138 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2025-04-15 19:25:40.491966 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2025-04-15 19:25:40.631958 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2025-04-15 19:25:40.767075 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2025-04-15 19:25:40.917506 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2025-04-15 19:25:41.068107 INFO::Fitting model to feature number 82, Escherichia.coli
## 2025-04-15 19:25:41.209729 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2025-04-15 19:25:41.344788 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:41.477457 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 19:25:41.614293 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2025-04-15 19:25:41.761626 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2025-04-15 19:25:41.940778 INFO::Counting total values for each feature
## 2025-04-15 19:25:41.969947 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2025-04-15 19:25:42.063554 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2025-04-15 19:25:42.158635 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2025-04-15 19:25:42.339636 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2025-04-15 19:25:42.395012 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2025-04-15 19:25:42.426726 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2025-04-15 19:25:42.431734 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2025-04-15 19:25:42.436445 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
## 2025-04-15 19:25:42.438699 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2025-04-15 19:25:42.642056 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2025-04-15 19:25:42.647626 INFO::Plotting associations from most to least significant, grouped by metadata
## 2025-04-15 19:25:42.648548 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2025-04-15 19:25:42.65 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2025-04-15 19:25:42.97705 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2025-04-15 19:25:43.259897 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2025-04-15 19:25:43.51336 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2025-04-15 19:25:43.75638 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2025-04-15 19:25:44.00944 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2025-04-15 19:25:44.280195 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2025-04-15 19:25:44.552767 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2025-04-15 19:25:44.8045 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2025-04-15 19:25:45.053552 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2025-04-15 19:25:45.302024 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2025-04-15 19:25:45.550259 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2025-04-15 19:25:45.796277 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2025-04-15 19:25:46.032407 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2025-04-15 19:25:46.284836 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2025-04-15 19:25:46.529086 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2025-04-15 19:25:46.835245 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2025-04-15 19:25:47.080825 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2025-04-15 19:25:47.329322 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2025-04-15 19:25:47.572007 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-15 19:25:47.840433 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2025-04-15 19:25:48.096912 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2025-04-15 19:25:48.356826 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2025-04-15 19:25:48.597581 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2025-04-15 19:25:48.84936 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2025-04-15 19:25:49.099095 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2025-04-15 19:25:49.354275 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2025-04-15 19:25:49.595255 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2025-04-15 19:25:49.846617 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2025-04-15 19:25:50.088463 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2025-04-15 19:25:50.335471 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2025-04-15 19:25:50.583034 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2025-04-15 19:25:50.841427 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2025-04-15 19:25:51.074912 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2025-04-15 19:25:51.330233 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2025-04-15 19:25:51.575015 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2025-04-15 19:25:51.820533 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2025-04-15 19:25:52.061351 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2025-04-15 19:25:52.312254 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2025-04-15 19:25:52.552836 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2025-04-15 19:25:52.799088 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2025-04-15 19:25:53.045536 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2025-04-15 19:25:53.298707 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2025-04-15 19:25:53.531078 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2025-04-15 19:25:53.785331 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2025-04-15 19:25:54.02594 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2025-04-15 19:25:54.278019 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2025-04-15 19:25:54.52552 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2025-04-15 19:25:54.782763 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2025-04-15 19:25:55.046102 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2025-04-15 19:25:55.296341 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2025-04-15 19:25:55.548095 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2025-04-15 19:25:55.79432 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2025-04-15 19:25:56.05229 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2025-04-15 19:25:56.286664 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2025-04-15 19:25:56.537128 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2025-04-15 19:25:56.776943 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2025-04-15 19:25:57.027559 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2025-04-15 19:25:57.259285 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2025-04-15 19:25:57.508878 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2025-04-15 19:25:57.744872 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2025-04-15 19:25:58.002509 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2025-04-15 19:25:58.234128 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2025-04-15 19:26:01.561057 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2025-04-15 19:26:01.563458 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2025-04-15 19:26:01.786158 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2025-04-15 19:26:02.044649 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2025-04-15 19:26:02.285989 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2025-04-15 19:26:02.527315 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2025-04-15 19:26:02.768573 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2025-04-15 19:26:03.019594 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2025-04-15 19:26:03.262601 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2025-04-15 19:26:03.525683 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2025-04-15 19:26:03.765965 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2025-04-15 19:26:04.014326 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2025-04-15 19:26:04.261643 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2025-04-15 19:26:04.516149 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-15 19:26:04.757303 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2025-04-15 19:26:05.006015 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2025-04-15 19:26:05.248454 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2025-04-15 19:26:05.501612 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2025-04-15 19:26:05.745215 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2025-04-15 19:26:05.996668 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2025-04-15 19:26:06.254785 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2025-04-15 19:26:06.512935 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2025-04-15 19:26:06.753873 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2025-04-15 19:26:06.998362 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2025-04-15 19:26:07.240484 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2025-04-15 19:26:07.48576 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2025-04-15 19:26:07.723467 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2025-04-15 19:26:07.970132 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2025-04-15 19:26:08.212999 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2025-04-15 19:26:08.452273 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2025-04-15 19:26:08.700004 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2025-04-15 19:26:08.939676 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2025-04-15 19:26:09.184328 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2025-04-15 19:26:09.432338 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2025-04-15 19:26:09.676801 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2025-04-15 19:26:09.928018 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2025-04-15 19:26:10.170792 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2025-04-15 19:26:10.413014 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2025-04-15 19:26:10.659849 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2025-04-15 19:26:10.911382 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2025-04-15 19:26:11.153258 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2025-04-15 19:26:11.416186 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2025-04-15 19:26:11.662612 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2025-04-15 19:26:11.963089 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2025-04-15 19:26:12.214312 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2025-04-15 19:26:15.340374 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2025-04-15 19:26:15.342459 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2025-04-15 19:26:15.573971 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2025-04-15 19:26:15.820626 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2025-04-15 19:26:16.079324 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2025-04-15 19:26:16.316279 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2025-04-15 19:26:16.56817 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-15 19:26:16.814362 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2025-04-15 19:26:17.068507 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2025-04-15 19:26:17.318934 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2025-04-15 19:26:17.569146 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2025-04-15 19:26:17.808291 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2025-04-15 19:26:18.058342 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2025-04-15 19:26:18.309165 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2025-04-15 19:26:18.56215 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2025-04-15 19:26:18.814261 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2025-04-15 19:26:19.080532 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2025-04-15 19:26:19.319763 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2025-04-15 19:26:19.567104 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2025-04-15 19:26:19.82997 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2025-04-15 19:26:20.067707 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2025-04-15 19:26:20.316252 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2025-04-15 19:26:20.561703 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2025-04-15 19:26:20.839029 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2025-04-15 19:26:21.108678 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2025-04-15 19:26:21.370242 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2025-04-15 19:26:21.614422 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2025-04-15 19:26:21.868875 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2025-04-15 19:26:22.107611 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2025-04-15 19:26:22.361593 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2025-04-15 19:26:25.503651 INFO::Plotting data for metadata number 4, antibiotics
## 2025-04-15 19:26:25.505515 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2025-04-15 19:26:25.714274 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2025-04-15 19:26:25.95588 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2025-04-15 19:26:26.186809 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2025-04-15 19:26:26.437994 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2025-04-15 19:26:26.669861 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2025-04-15 19:26:26.91607 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2025-04-15 19:26:27.150525 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2025-04-15 19:26:27.392191 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2025-04-15 19:26:27.626262 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2025-04-15 19:26:27.878144 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2025-04-15 19:26:28.103022 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2025-04-15 19:26:28.355728 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2025-04-15 19:26:28.59515 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2025-04-15 19:26:28.845532 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2025-04-15 19:26:29.080175 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-15 19:26:29.334408 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2025-04-15 19:26:29.56737 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2025-04-15 19:26:29.809803 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2025-04-15 19:26:30.038362 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2025-04-15 19:26:30.293405 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2025-04-15 19:26:30.533804 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2025-04-15 19:26:30.779887 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2025-04-15 19:26:31.016404 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2025-04-15 19:26:31.259499 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2025-04-15 19:26:31.494316 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2025-04-15 19:26:31.737648 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2025-04-15 19:26:31.973289 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2025-04-15 19:26:32.216547 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2025-04-15 19:26:32.472543 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2025-04-15 19:26:32.736798 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2025-04-15 19:26:32.964647 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2025-04-15 19:26:33.203286 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2025-04-15 19:26:33.722454 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2025-04-15 19:26:33.945078 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2025-04-15 19:26:34.169696 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2025-04-15 19:26:34.393401 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2025-04-15 19:26:34.615897 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2025-04-15 19:26:34.842368 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2025-04-15 19:26:35.066443 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2025-04-15 19:26:37.900285 INFO::Plotting data for metadata number 5, age
## 2025-04-15 19:26:37.902237 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()`).
## 2025-04-15 19:26:38.15375 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()`).
## 2025-04-15 19:26:38.462534 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()`).
## 2025-04-15 19:26:38.69715 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()`).
## 2025-04-15 19:26:38.933434 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()`).
## 2025-04-15 19:26:39.156181 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()`).
## 2025-04-15 19:26:39.386649 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()`).
## 2025-04-15 19:26:39.618466 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()`).
## 2025-04-15 19:26:39.848486 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()`).
## 2025-04-15 19:26:40.097565 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()`).
## 2025-04-15 19:26:40.346146 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()`).
## 2025-04-15 19:26:40.570121 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()`).
## 2025-04-15 19:26:40.805714 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()`).
## 2025-04-15 19:26:41.046853 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()`).
## 2025-04-15 19:26:41.268546 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()`).
## 2025-04-15 19:26:41.493959 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()`).
## 2025-04-15 19:26:41.721192 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()`).
## 2025-04-15 19:26:41.950976 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()`).
## 2025-04-15 19:26:42.180192 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()`).
## 2025-04-15 19:26:42.404857 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()`).
## 2025-04-15 19:26:42.644688 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()`).
## 2025-04-15 19:26:42.87433 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()`).
## 2025-04-15 19:26:45.953499 INFO::Plotting data for metadata number 6, diagnosis
## 2025-04-15 19:26:45.955369 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2025-04-15 19:26:46.184333 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2025-04-15 19:26:46.427822 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2025-04-15 19:26:46.689075 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2025-04-15 19:26:46.940392 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2025-04-15 19:26:47.207814 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2025-04-15 19:26:47.467937 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2025-04-15 19:26:47.721653 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2025-04-15 19:26:47.967894 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2025-04-15 19:26:48.227972 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2025-04-15 19:26:48.470075 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2025-04-15 19:26:48.728366 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2025-04-15 19:26:48.978231 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2025-04-15 19:26:49.233431 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2025-04-15 19:26:49.477823 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2025-04-15 19:26:49.733722 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2025-04-15 19:26:49.988169 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2025-04-15 19:26:50.240885 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2025-04-15 19:26:50.503075 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2025-04-15 19:26:50.74452 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2025-04-15 19:26:51.003051 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2025-04-15 19:26:51.245179 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2025-04-15 19:26:51.500253 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2025-04-15 19:26:51.75016 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2025-04-15 19:26:52.004594 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2025-04-15 19:26:52.261485 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2025-04-15 19:26:52.499691 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2025-04-15 19:26:52.768445 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2025-04-15 19:26:53.014526 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2025-04-15 19:26:53.270968 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2025-04-15 19:26:53.518354 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2025-04-15 19:26:53.835284 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2025-04-15 19:26:54.086661 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2025-04-15 19:26:54.357739 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2025-04-15 19:26:54.613508 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2025-04-15 19:26:54.868453 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2025-04-15 19:26:55.121481 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2025-04-15 19:26:55.368464 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2025-04-15 19:26:55.625289 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2025-04-15 19:26:55.864654 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2025-04-15 19:26:56.115635 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2025-04-15 19:26:56.359583 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2025-04-15 19:26:56.613289 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 beta (2025-04-02 r88102)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## 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     farver_2.1.2       
## [25] compiler_4.5.0      munsell_0.5.1       lmerTest_3.1-3     
## [28] permute_0.9-7       htmltools_0.5.8.1   sass_0.4.10        
## [31] hash_2.2.6.3        yaml_2.3.10         pillar_1.10.2      
## [34] nloptr_2.2.1        crayon_1.5.3        jquerylib_0.1.4    
## [37] MASS_7.3-65         cachem_1.1.0        vegan_2.6-10       
## [40] reformulas_0.4.0    boot_1.3-31         nlme_3.1-168       
## [43] robustbase_0.99-4-1 tidyselect_1.2.1    digest_0.6.37      
## [46] mvtnorm_1.3-3       dplyr_1.1.4         labeling_0.4.3     
## [49] splines_4.5.0       pcaPP_2.0-5         fastmap_1.2.0      
## [52] grid_4.5.0          colorspace_2.1-1    cli_3.6.4          
## [55] magrittr_2.0.3      withr_3.0.2         scales_1.3.0       
## [58] rmarkdown_2.29      lme4_1.1-37         pbapply_1.7-2      
## [61] evaluate_1.0.3      knitr_1.50          rbibutils_2.3      
## [64] mgcv_1.9-3          rlang_1.1.6         Rcpp_1.0.14        
## [67] glue_1.8.0          optparse_1.7.5      DBI_1.2.3          
## [70] minqa_1.2.8         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.