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"
## 2025-01-02 17:53:47.202081 INFO::Writing function arguments to log file
## 2025-01-02 17:53:47.225626 INFO::Verifying options selected are valid
## 2025-01-02 17:53:47.255648 INFO::Determining format of input files
## 2025-01-02 17:53:47.256723 INFO::Input format is data samples as rows and metadata samples as rows
## 2025-01-02 17:53:47.260533 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2025-01-02 17:53:47.261473 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2025-01-02 17:53:47.263451 INFO::Filter data based on min abundance and min prevalence
## 2025-01-02 17:53:47.264083 INFO::Total samples in data: 1595
## 2025-01-02 17:53:47.264687 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2025-01-02 17:53:47.269398 INFO::Total filtered features: 0
## 2025-01-02 17:53:47.270136 INFO::Filtered feature names from abundance and prevalence filtering:
## 2025-01-02 17:53:47.278503 INFO::Total filtered features with variance filtering: 0
## 2025-01-02 17:53:47.279237 INFO::Filtered feature names from variance filtering:
## 2025-01-02 17:53:47.279843 INFO::Running selected normalization method: TSS
## 2025-01-02 17:53:48.274768 INFO::Bypass z-score application to metadata
## 2025-01-02 17:53:48.275735 INFO::Running selected transform method: LOG
## 2025-01-02 17:53:48.293063 INFO::Running selected analysis method: LM
## 2025-01-02 17:53:48.563244 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:48.860132 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2025-01-02 17:53:49.079124 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2025-01-02 17:53:49.414629 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:49.548068 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2025-01-02 17:53:49.713017 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:49.869003 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2025-01-02 17:53:50.004932 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2025-01-02 17:53:50.145398 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2025-01-02 17:53:50.278923 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2025-01-02 17:53:50.422205 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
## 2025-01-02 17:53:50.531813 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
## 2025-01-02 17:53:50.668744 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:50.802887 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:50.947237 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2025-01-02 17:53:51.078686 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:51.205524 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2025-01-02 17:53:51.348777 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2025-01-02 17:53:51.483063 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:51.615717 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:51.761181 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:51.895614 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:52.033729 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2025-01-02 17:53:52.165695 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2025-01-02 17:53:52.318126 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2025-01-02 17:53:52.476427 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2025-01-02 17:53:52.613103 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:52.767889 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2025-01-02 17:53:52.905655 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2025-01-02 17:53:53.047258 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:53.190721 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2025-01-02 17:53:53.326128 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2025-01-02 17:53:53.457875 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:53.594939 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:53.724706 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:53.860564 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:53.999466 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2025-01-02 17:53:54.136624 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2025-01-02 17:53:54.498164 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2025-01-02 17:53:54.639645 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:54.782213 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
## 2025-01-02 17:53:54.900892 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
## 2025-01-02 17:53:55.046882 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:55.175807 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:55.308779 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2025-01-02 17:53:55.459336 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2025-01-02 17:53:55.59016 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:55.72196 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:55.863451 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2025-01-02 17:53:55.993601 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2025-01-02 17:53:56.12992 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:56.281505 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:56.422437 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:56.554015 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:56.679889 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:56.817922 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2025-01-02 17:53:56.947431 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2025-01-02 17:53:57.077939 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2025-01-02 17:53:57.230991 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:57.376373 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:57.518807 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:57.669463 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:57.803953 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2025-01-02 17:53:57.93784 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:58.06766 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:58.201097 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2025-01-02 17:53:58.343037 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2025-01-02 17:53:58.47974 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2025-01-02 17:53:58.612348 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:58.736364 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2025-01-02 17:53:58.87037 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2025-01-02 17:53:59.003871 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:59.135355 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2025-01-02 17:53:59.269592 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2025-01-02 17:53:59.401832 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:59.528927 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2025-01-02 17:53:59.66855 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:59.800235 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:53:59.928028 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2025-01-02 17:54:00.301643 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2025-01-02 17:54:00.434713 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2025-01-02 17:54:00.565817 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2025-01-02 17:54:00.706871 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2025-01-02 17:54:00.846256 INFO::Fitting model to feature number 82, Escherichia.coli
## 2025-01-02 17:54:00.980595 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2025-01-02 17:54:01.111047 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:54:01.236574 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2025-01-02 17:54:01.367179 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2025-01-02 17:54:01.501199 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2025-01-02 17:54:01.673002 INFO::Counting total values for each feature
## 2025-01-02 17:54:01.701156 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2025-01-02 17:54:01.794098 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2025-01-02 17:54:01.88879 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2025-01-02 17:54:02.064705 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2025-01-02 17:54:02.119647 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2025-01-02 17:54:02.151088 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2025-01-02 17:54:02.156015 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2025-01-02 17:54:02.166996 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
## 2025-01-02 17:54:02.169502 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2025-01-02 17:54:02.365796 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2025-01-02 17:54:02.371086 INFO::Plotting associations from most to least significant, grouped by metadata
## 2025-01-02 17:54:02.371975 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2025-01-02 17:54:02.3734 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2025-01-02 17:54:02.683927 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2025-01-02 17:54:02.950544 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2025-01-02 17:54:03.185878 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2025-01-02 17:54:03.42413 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2025-01-02 17:54:03.653424 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2025-01-02 17:54:03.888585 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2025-01-02 17:54:04.117332 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2025-01-02 17:54:04.352727 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2025-01-02 17:54:04.583587 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2025-01-02 17:54:04.818772 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2025-01-02 17:54:05.049778 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2025-01-02 17:54:05.286272 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2025-01-02 17:54:05.539414 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2025-01-02 17:54:05.792913 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2025-01-02 17:54:06.025922 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2025-01-02 17:54:06.261362 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2025-01-02 17:54:06.49962 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2025-01-02 17:54:06.732911 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2025-01-02 17:54:06.962914 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-01-02 17:54:07.198337 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2025-01-02 17:54:07.433587 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2025-01-02 17:54:07.671834 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2025-01-02 17:54:07.892638 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2025-01-02 17:54:08.126616 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2025-01-02 17:54:08.356009 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2025-01-02 17:54:08.593249 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2025-01-02 17:54:08.820518 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2025-01-02 17:54:09.072132 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2025-01-02 17:54:09.315075 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2025-01-02 17:54:09.54446 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2025-01-02 17:54:09.771819 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2025-01-02 17:54:09.99799 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2025-01-02 17:54:10.268431 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2025-01-02 17:54:10.494075 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2025-01-02 17:54:10.745769 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2025-01-02 17:54:10.97064 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2025-01-02 17:54:11.21064 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2025-01-02 17:54:11.438685 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2025-01-02 17:54:11.670181 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2025-01-02 17:54:11.89093 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2025-01-02 17:54:12.118247 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2025-01-02 17:54:12.353997 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2025-01-02 17:54:12.574434 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2025-01-02 17:54:12.810294 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2025-01-02 17:54:13.035908 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2025-01-02 17:54:13.266418 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2025-01-02 17:54:13.492814 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2025-01-02 17:54:13.721717 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2025-01-02 17:54:13.955451 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2025-01-02 17:54:14.190399 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2025-01-02 17:54:14.42005 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2025-01-02 17:54:14.669009 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2025-01-02 17:54:14.898838 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2025-01-02 17:54:15.13221 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2025-01-02 17:54:15.35999 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2025-01-02 17:54:15.597533 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2025-01-02 17:54:15.826306 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2025-01-02 17:54:16.057573 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2025-01-02 17:54:16.283496 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2025-01-02 17:54:16.519964 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2025-01-02 17:54:16.752124 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2025-01-02 17:54:16.983098 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2025-01-02 17:54:19.960769 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2025-01-02 17:54:19.962584 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2025-01-02 17:54:20.163991 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2025-01-02 17:54:20.413402 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2025-01-02 17:54:20.649726 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2025-01-02 17:54:20.893107 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2025-01-02 17:54:21.127645 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2025-01-02 17:54:21.376109 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2025-01-02 17:54:21.60613 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2025-01-02 17:54:21.890559 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2025-01-02 17:54:22.123892 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2025-01-02 17:54:22.369545 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2025-01-02 17:54:22.610917 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2025-01-02 17:54:22.86316 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-01-02 17:54:23.096756 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2025-01-02 17:54:23.341943 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2025-01-02 17:54:23.577568 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2025-01-02 17:54:23.826837 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2025-01-02 17:54:24.060793 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2025-01-02 17:54:24.305789 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2025-01-02 17:54:24.53619 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2025-01-02 17:54:24.785133 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2025-01-02 17:54:25.027198 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2025-01-02 17:54:25.268857 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2025-01-02 17:54:25.502371 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2025-01-02 17:54:25.745381 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2025-01-02 17:54:25.984453 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2025-01-02 17:54:26.258795 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2025-01-02 17:54:26.485092 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2025-01-02 17:54:26.723437 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2025-01-02 17:54:26.950457 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2025-01-02 17:54:27.191172 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2025-01-02 17:54:27.4157 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2025-01-02 17:54:27.664993 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2025-01-02 17:54:27.893107 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2025-01-02 17:54:28.145373 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2025-01-02 17:54:28.381862 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2025-01-02 17:54:28.619658 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2025-01-02 17:54:28.872146 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2025-01-02 17:54:29.122994 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2025-01-02 17:54:29.36742 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2025-01-02 17:54:29.603391 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2025-01-02 17:54:29.852732 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2025-01-02 17:54:30.092998 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2025-01-02 17:54:30.334912 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2025-01-02 17:54:33.618177 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2025-01-02 17:54:33.619897 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2025-01-02 17:54:33.816178 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2025-01-02 17:54:34.05095 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2025-01-02 17:54:34.283353 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2025-01-02 17:54:34.511552 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2025-01-02 17:54:34.741067 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-01-02 17:54:34.981652 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2025-01-02 17:54:35.216146 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2025-01-02 17:54:35.460569 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2025-01-02 17:54:35.69383 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2025-01-02 17:54:35.92814 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2025-01-02 17:54:36.155414 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2025-01-02 17:54:36.400336 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2025-01-02 17:54:36.626112 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2025-01-02 17:54:36.867695 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2025-01-02 17:54:37.099599 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2025-01-02 17:54:37.32984 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2025-01-02 17:54:37.553899 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2025-01-02 17:54:37.793015 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2025-01-02 17:54:38.012428 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2025-01-02 17:54:38.244636 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2025-01-02 17:54:38.470713 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2025-01-02 17:54:38.707785 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2025-01-02 17:54:38.936377 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2025-01-02 17:54:39.172109 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2025-01-02 17:54:39.400656 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2025-01-02 17:54:39.671335 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2025-01-02 17:54:39.907708 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2025-01-02 17:54:40.140326 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2025-01-02 17:54:43.021756 INFO::Plotting data for metadata number 4, antibiotics
## 2025-01-02 17:54:43.0236 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2025-01-02 17:54:43.252022 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2025-01-02 17:54:43.473011 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2025-01-02 17:54:43.69678 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2025-01-02 17:54:43.935367 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2025-01-02 17:54:44.154152 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2025-01-02 17:54:44.390475 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2025-01-02 17:54:44.609811 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2025-01-02 17:54:44.835316 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2025-01-02 17:54:45.049205 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2025-01-02 17:54:45.285106 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2025-01-02 17:54:45.514048 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2025-01-02 17:54:45.743828 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2025-01-02 17:54:45.982773 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2025-01-02 17:54:46.199495 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2025-01-02 17:54:46.42993 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-01-02 17:54:46.647834 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2025-01-02 17:54:46.880447 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2025-01-02 17:54:47.092726 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2025-01-02 17:54:47.318075 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2025-01-02 17:54:47.535713 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2025-01-02 17:54:47.777216 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2025-01-02 17:54:47.991164 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2025-01-02 17:54:48.229015 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2025-01-02 17:54:48.44739 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2025-01-02 17:54:48.680697 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2025-01-02 17:54:48.897461 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2025-01-02 17:54:49.11604 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2025-01-02 17:54:49.340193 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2025-01-02 17:54:49.563412 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2025-01-02 17:54:49.793558 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2025-01-02 17:54:50.007638 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2025-01-02 17:54:50.23379 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2025-01-02 17:54:50.446527 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2025-01-02 17:54:50.672505 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2025-01-02 17:54:50.88657 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2025-01-02 17:54:51.112572 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2025-01-02 17:54:51.328578 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2025-01-02 17:54:51.56722 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2025-01-02 17:54:51.779634 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2025-01-02 17:54:54.629619 INFO::Plotting data for metadata number 5, age
## 2025-01-02 17:54:54.631319 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()`).
## 2025-01-02 17:54:54.884345 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()`).
## 2025-01-02 17:54:55.176123 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()`).
## 2025-01-02 17:54:55.399838 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()`).
## 2025-01-02 17:54:55.633675 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()`).
## 2025-01-02 17:54:55.863922 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()`).
## 2025-01-02 17:54:56.101175 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()`).
## 2025-01-02 17:54:56.338542 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()`).
## 2025-01-02 17:54:56.571083 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()`).
## 2025-01-02 17:54:56.79417 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()`).
## 2025-01-02 17:54:57.030056 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()`).
## 2025-01-02 17:54:57.25167 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()`).
## 2025-01-02 17:54:57.488399 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()`).
## 2025-01-02 17:54:57.722803 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()`).
## 2025-01-02 17:54:57.940745 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()`).
## 2025-01-02 17:54:58.169328 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()`).
## 2025-01-02 17:54:58.396025 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()`).
## 2025-01-02 17:54:58.623331 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()`).
## 2025-01-02 17:54:58.849432 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()`).
## 2025-01-02 17:54:59.071881 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()`).
## 2025-01-02 17:54:59.306361 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()`).
## 2025-01-02 17:54:59.526735 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()`).
## 2025-01-02 17:55:02.464429 INFO::Plotting data for metadata number 6, diagnosis
## 2025-01-02 17:55:02.466106 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2025-01-02 17:55:02.679434 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2025-01-02 17:55:02.906544 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2025-01-02 17:55:03.18072 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2025-01-02 17:55:03.419443 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2025-01-02 17:55:03.667753 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2025-01-02 17:55:03.898406 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2025-01-02 17:55:04.148293 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2025-01-02 17:55:04.383165 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2025-01-02 17:55:04.627155 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2025-01-02 17:55:04.862705 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2025-01-02 17:55:05.118611 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2025-01-02 17:55:05.352853 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2025-01-02 17:55:05.596909 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2025-01-02 17:55:05.830396 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2025-01-02 17:55:06.082833 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2025-01-02 17:55:06.309529 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2025-01-02 17:55:06.561935 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2025-01-02 17:55:06.802682 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2025-01-02 17:55:07.056237 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2025-01-02 17:55:07.284544 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2025-01-02 17:55:07.537072 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2025-01-02 17:55:07.780059 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2025-01-02 17:55:08.022464 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2025-01-02 17:55:08.265067 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2025-01-02 17:55:08.494728 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2025-01-02 17:55:08.738477 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2025-01-02 17:55:08.974543 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2025-01-02 17:55:09.223294 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2025-01-02 17:55:09.455173 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2025-01-02 17:55:09.702129 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2025-01-02 17:55:09.931267 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2025-01-02 17:55:10.172501 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2025-01-02 17:55:10.405495 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2025-01-02 17:55:10.653735 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2025-01-02 17:55:10.904924 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2025-01-02 17:55:11.133443 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2025-01-02 17:55:11.38161 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2025-01-02 17:55:11.640799 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2025-01-02 17:55:11.891446 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2025-01-02 17:55:12.120442 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2025-01-02 17:55:12.399261 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2025-01-02 17:55:12.686818 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 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.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_1.20.0
## 
## loaded via a namespace (and not attached):
##  [1] sass_0.4.9          generics_0.1.3      robustbase_0.99-4-1
##  [4] lattice_0.22-6      lme4_1.1-35.5       digest_0.6.37      
##  [7] magrittr_2.0.3      RColorBrewer_1.1-3  evaluate_1.0.1     
## [10] grid_4.4.2          mvtnorm_1.3-2       fastmap_1.2.0      
## [13] jsonlite_1.8.9      Matrix_1.7-1        DBI_1.2.3          
## [16] optparse_1.7.5      biglm_0.9-3         mgcv_1.9-1         
## [19] scales_1.3.0        pbapply_1.7-2       permute_0.9-7      
## [22] numDeriv_2016.8-1.1 getopt_1.20.4       jquerylib_0.1.4    
## [25] cli_3.6.3           rlang_1.1.4         crayon_1.5.3       
## [28] munsell_0.5.1       splines_4.4.2       withr_3.0.2        
## [31] cachem_1.1.0        yaml_2.3.10         vegan_2.6-8        
## [34] tools_4.4.2         parallel_4.4.2      nloptr_2.1.1       
## [37] minqa_1.2.8         dplyr_1.1.4         colorspace_2.1-1   
## [40] ggplot2_3.5.1       boot_1.3-31         hash_2.2.6.3       
## [43] vctrs_0.6.5         R6_2.5.1            lifecycle_1.0.4    
## [46] MASS_7.3-63         logging_0.10-108    pcaPP_2.0-5        
## [49] cluster_2.1.8       pkgconfig_2.0.3     gtable_0.3.6       
## [52] lmerTest_3.1-3      pillar_1.10.0       bslib_0.8.0        
## [55] Rcpp_1.0.13-1       data.table_1.16.4   glue_1.8.0         
## [58] DEoptimR_1.1-3-1    xfun_0.49           tibble_3.2.1       
## [61] tidyselect_1.2.1    knitr_1.49          farver_2.1.2       
## [64] htmltools_0.5.8.1   nlme_3.1-166        labeling_0.4.3     
## [67] rmarkdown_2.29      pheatmap_1.0.12     compiler_4.4.2

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.