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"
## 2024-05-01 01:24:27.744276 INFO::Writing function arguments to log file
## 2024-05-01 01:24:27.754651 INFO::Verifying options selected are valid
## 2024-05-01 01:24:27.770424 INFO::Determining format of input files
## 2024-05-01 01:24:27.770894 INFO::Input format is data samples as rows and metadata samples as rows
## 2024-05-01 01:24:27.77275 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2024-05-01 01:24:27.773164 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2024-05-01 01:24:27.773954 INFO::Filter data based on min abundance and min prevalence
## 2024-05-01 01:24:27.774194 INFO::Total samples in data: 1595
## 2024-05-01 01:24:27.774426 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2024-05-01 01:24:27.776069 INFO::Total filtered features: 0
## 2024-05-01 01:24:27.776347 INFO::Filtered feature names from abundance and prevalence filtering:
## 2024-05-01 01:24:27.779197 INFO::Total filtered features with variance filtering: 0
## 2024-05-01 01:24:27.779461 INFO::Filtered feature names from variance filtering:
## 2024-05-01 01:24:27.779669 INFO::Running selected normalization method: TSS
## 2024-05-01 01:24:28.173906 INFO::Bypass z-score application to metadata
## 2024-05-01 01:24:28.174358 INFO::Running selected transform method: LOG
## 2024-05-01 01:24:28.18097 INFO::Running selected analysis method: LM
## 2024-05-01 01:24:28.287486 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:28.402816 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2024-05-01 01:24:28.459179 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2024-05-01 01:24:28.508548 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:28.583816 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2024-05-01 01:24:28.6354 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:28.684993 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2024-05-01 01:24:28.734976 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2024-05-01 01:24:28.787755 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2024-05-01 01:24:28.834527 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2024-05-01 01:24:28.88495 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:28.935019 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:28.982208 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:29.034059 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2024-05-01 01:24:29.08446 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:29.132379 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2024-05-01 01:24:29.180144 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2024-05-01 01:24:29.230393 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## Feature Bacteroides.thetaiotaomicron : simpleWarning: Model failed to converge with 1 negative eigenvalue: -5.1e+00
## 2024-05-01 01:24:29.271607 WARNING::Fitting problem for feature 18 a warning was issued
## boundary (singular) fit: see help('isSingular')
## Warning: Model failed to converge with 1 negative eigenvalue: -5.1e+00
## 2024-05-01 01:24:29.317836 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:29.368339 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:29.41906 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:29.469087 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2024-05-01 01:24:29.514556 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2024-05-01 01:24:29.649737 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2024-05-01 01:24:29.699577 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2024-05-01 01:24:29.750404 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:29.803099 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2024-05-01 01:24:29.850831 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2024-05-01 01:24:29.898848 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:29.944868 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2024-05-01 01:24:30.086384 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2024-05-01 01:24:30.132576 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:30.17859 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:30.227203 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:30.274853 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:30.321333 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2024-05-01 01:24:30.369733 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2024-05-01 01:24:30.418259 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2024-05-01 01:24:30.466224 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:30.515775 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:30.565472 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:30.610325 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:30.656134 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2024-05-01 01:24:30.801713 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2024-05-01 01:24:30.847384 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:30.89332 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:30.944991 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2024-05-01 01:24:30.995061 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2024-05-01 01:24:31.043442 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.093259 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.141546 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.187606 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.232667 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.283048 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2024-05-01 01:24:31.329805 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2024-05-01 01:24:31.376597 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2024-05-01 01:24:31.428563 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.476088 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.529201 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.585582 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.632619 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2024-05-01 01:24:31.675977 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.726605 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.773112 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2024-05-01 01:24:31.823296 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2024-05-01 01:24:31.870595 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2024-05-01 01:24:31.922817 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:31.96756 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2024-05-01 01:24:32.013672 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2024-05-01 01:24:32.066021 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:32.1167 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2024-05-01 01:24:32.16506 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2024-05-01 01:24:32.217011 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:32.263722 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2024-05-01 01:24:32.311614 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:32.362039 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:32.408207 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2024-05-01 01:24:32.454579 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2024-05-01 01:24:32.505825 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2024-05-01 01:24:32.554871 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2024-05-01 01:24:32.609348 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2024-05-01 01:24:32.667486 INFO::Fitting model to feature number 82, Escherichia.coli
## 2024-05-01 01:24:32.718371 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2024-05-01 01:24:32.765921 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:32.810954 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2024-05-01 01:24:32.859596 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2024-05-01 01:24:32.910474 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2024-05-01 01:24:32.973072 INFO::Counting total values for each feature
## 2024-05-01 01:24:32.989375 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2024-05-01 01:24:33.037372 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2024-05-01 01:24:33.093201 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2024-05-01 01:24:33.168193 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2024-05-01 01:24:33.197842 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2024-05-01 01:24:33.214273 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2024-05-01 01:24:33.217256 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2024-05-01 01:24:33.219959 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
## 2024-05-01 01:24:33.221177 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2024-05-01 01:24:33.277706 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2024-05-01 01:24:33.280488 INFO::Plotting associations from most to least significant, grouped by metadata
## 2024-05-01 01:24:33.280881 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2024-05-01 01:24:33.281545 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2024-05-01 01:24:33.402671 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2024-05-01 01:24:33.503721 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2024-05-01 01:24:33.594995 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2024-05-01 01:24:33.683612 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2024-05-01 01:24:33.771533 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2024-05-01 01:24:33.849564 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2024-05-01 01:24:33.931103 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2024-05-01 01:24:34.010687 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2024-05-01 01:24:34.113432 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2024-05-01 01:24:34.202007 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2024-05-01 01:24:34.291221 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2024-05-01 01:24:34.368293 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2024-05-01 01:24:34.4494 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2024-05-01 01:24:34.526855 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2024-05-01 01:24:34.612287 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2024-05-01 01:24:34.690598 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2024-05-01 01:24:34.780724 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2024-05-01 01:24:34.859355 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2024-05-01 01:24:34.943456 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-05-01 01:24:35.025249 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2024-05-01 01:24:35.117416 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2024-05-01 01:24:35.198322 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2024-05-01 01:24:35.290232 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2024-05-01 01:24:35.370507 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2024-05-01 01:24:35.452847 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2024-05-01 01:24:35.532474 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2024-05-01 01:24:35.614162 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2024-05-01 01:24:35.692022 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2024-05-01 01:24:35.775416 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2024-05-01 01:24:35.850386 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2024-05-01 01:24:35.933762 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2024-05-01 01:24:36.010434 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2024-05-01 01:24:36.096718 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2024-05-01 01:24:36.178952 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2024-05-01 01:24:36.26674 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2024-05-01 01:24:36.34418 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2024-05-01 01:24:36.427152 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2024-05-01 01:24:36.50731 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2024-05-01 01:24:36.584075 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2024-05-01 01:24:36.663874 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2024-05-01 01:24:36.741855 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2024-05-01 01:24:36.830317 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2024-05-01 01:24:36.909431 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2024-05-01 01:24:36.998196 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2024-05-01 01:24:37.082178 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2024-05-01 01:24:37.169288 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2024-05-01 01:24:37.250342 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2024-05-01 01:24:37.324784 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2024-05-01 01:24:37.400141 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2024-05-01 01:24:37.474988 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2024-05-01 01:24:37.545328 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2024-05-01 01:24:37.6242 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2024-05-01 01:24:37.700766 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2024-05-01 01:24:37.769378 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2024-05-01 01:24:37.84863 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2024-05-01 01:24:37.922408 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2024-05-01 01:24:38.000884 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2024-05-01 01:24:38.074341 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2024-05-01 01:24:38.164459 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2024-05-01 01:24:38.245839 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2024-05-01 01:24:38.337239 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2024-05-01 01:24:38.450328 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-05-01 01:24:39.354246 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2024-05-01 01:24:39.355074 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2024-05-01 01:24:39.421753 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2024-05-01 01:24:39.513565 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2024-05-01 01:24:39.599982 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2024-05-01 01:24:39.693283 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2024-05-01 01:24:39.78283 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2024-05-01 01:24:39.87658 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2024-05-01 01:24:39.958204 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2024-05-01 01:24:40.052881 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2024-05-01 01:24:40.141543 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2024-05-01 01:24:40.234027 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2024-05-01 01:24:40.32682 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2024-05-01 01:24:40.420778 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-05-01 01:24:40.507051 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2024-05-01 01:24:40.597153 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2024-05-01 01:24:40.670558 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2024-05-01 01:24:40.750973 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2024-05-01 01:24:40.823612 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2024-05-01 01:24:40.903297 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2024-05-01 01:24:40.981073 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2024-05-01 01:24:41.055229 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2024-05-01 01:24:41.135937 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2024-05-01 01:24:41.210564 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2024-05-01 01:24:41.290475 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2024-05-01 01:24:41.365155 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2024-05-01 01:24:41.445914 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2024-05-01 01:24:41.522084 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2024-05-01 01:24:41.601347 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2024-05-01 01:24:41.680562 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2024-05-01 01:24:41.760928 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2024-05-01 01:24:41.8449 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2024-05-01 01:24:41.918788 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2024-05-01 01:24:42.133603 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2024-05-01 01:24:42.216506 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2024-05-01 01:24:42.309091 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2024-05-01 01:24:42.387421 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2024-05-01 01:24:42.466585 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2024-05-01 01:24:42.548237 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2024-05-01 01:24:42.626432 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2024-05-01 01:24:42.703194 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2024-05-01 01:24:42.785129 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2024-05-01 01:24:42.863589 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2024-05-01 01:24:42.946769 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2024-05-01 01:24:43.028358 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2024-05-01 01:24:43.853749 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2024-05-01 01:24:43.854541 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2024-05-01 01:24:43.916344 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2024-05-01 01:24:43.989368 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2024-05-01 01:24:44.065091 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2024-05-01 01:24:44.133158 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2024-05-01 01:24:44.209077 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-05-01 01:24:44.28944 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2024-05-01 01:24:44.361374 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2024-05-01 01:24:44.441856 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2024-05-01 01:24:44.513928 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2024-05-01 01:24:44.587344 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2024-05-01 01:24:44.658157 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2024-05-01 01:24:44.73466 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2024-05-01 01:24:44.805653 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2024-05-01 01:24:44.881894 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2024-05-01 01:24:44.955514 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2024-05-01 01:24:45.025193 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2024-05-01 01:24:45.097725 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2024-05-01 01:24:45.170879 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2024-05-01 01:24:45.259194 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2024-05-01 01:24:45.330031 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2024-05-01 01:24:45.409727 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2024-05-01 01:24:45.484047 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2024-05-01 01:24:45.569443 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2024-05-01 01:24:45.645394 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2024-05-01 01:24:45.731414 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2024-05-01 01:24:45.810504 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2024-05-01 01:24:45.89167 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2024-05-01 01:24:45.969483 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2024-05-01 01:24:46.853916 INFO::Plotting data for metadata number 4, antibiotics
## 2024-05-01 01:24:46.854713 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2024-05-01 01:24:46.921911 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2024-05-01 01:24:47.002051 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2024-05-01 01:24:47.088847 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2024-05-01 01:24:47.169589 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2024-05-01 01:24:47.256979 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2024-05-01 01:24:47.336634 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2024-05-01 01:24:47.42307 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2024-05-01 01:24:47.498861 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2024-05-01 01:24:47.585079 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2024-05-01 01:24:47.668796 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2024-05-01 01:24:47.758566 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2024-05-01 01:24:47.835275 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2024-05-01 01:24:47.923736 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2024-05-01 01:24:48.002483 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2024-05-01 01:24:48.088345 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-05-01 01:24:48.165107 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2024-05-01 01:24:48.25288 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2024-05-01 01:24:48.329494 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2024-05-01 01:24:48.411293 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2024-05-01 01:24:48.490622 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2024-05-01 01:24:48.578933 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2024-05-01 01:24:48.703166 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2024-05-01 01:24:48.788362 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2024-05-01 01:24:48.866702 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2024-05-01 01:24:48.948037 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2024-05-01 01:24:49.014715 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2024-05-01 01:24:49.100627 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2024-05-01 01:24:49.176308 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2024-05-01 01:24:49.263033 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2024-05-01 01:24:49.335747 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2024-05-01 01:24:49.422522 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2024-05-01 01:24:49.498341 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2024-05-01 01:24:49.578925 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2024-05-01 01:24:49.652384 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2024-05-01 01:24:49.734235 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2024-05-01 01:24:49.812326 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-05-01 01:24:49.901293 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2024-05-01 01:24:49.985416 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2024-05-01 01:24:50.078608 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2024-05-01 01:24:50.938092 INFO::Plotting data for metadata number 5, age
## 2024-05-01 01:24:50.938904 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()`).
## 2024-05-01 01:24:51.029962 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()`).
## 2024-05-01 01:24:51.145009 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()`).
## 2024-05-01 01:24:51.23037 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()`).
## 2024-05-01 01:24:51.325928 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()`).
## 2024-05-01 01:24:51.406485 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()`).
## 2024-05-01 01:24:51.494811 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()`).
## 2024-05-01 01:24:51.581086 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()`).
## 2024-05-01 01:24:51.671265 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()`).
## 2024-05-01 01:24:51.758803 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()`).
## 2024-05-01 01:24:51.838895 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()`).
## 2024-05-01 01:24:51.925085 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()`).
## 2024-05-01 01:24:52.037749 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()`).
## 2024-05-01 01:24:52.113588 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()`).
## 2024-05-01 01:24:52.195724 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()`).
## 2024-05-01 01:24:52.270212 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()`).
## 2024-05-01 01:24:52.359195 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()`).
## 2024-05-01 01:24:52.448613 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()`).
## 2024-05-01 01:24:52.527066 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()`).
## 2024-05-01 01:24:52.614735 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()`).
## 2024-05-01 01:24:52.706216 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()`).
## 2024-05-01 01:24:52.794589 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()`).
## 2024-05-01 01:24:53.747523 INFO::Plotting data for metadata number 6, diagnosis
## 2024-05-01 01:24:53.748309 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2024-05-01 01:24:53.827998 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-05-01 01:24:53.912616 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-05-01 01:24:54.007629 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-05-01 01:24:54.099736 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-05-01 01:24:54.192219 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2024-05-01 01:24:54.29471 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-05-01 01:24:54.383771 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-05-01 01:24:54.479019 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-05-01 01:24:54.563308 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-05-01 01:24:54.660526 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2024-05-01 01:24:54.760456 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-05-01 01:24:54.861738 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-05-01 01:24:54.960907 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-05-01 01:24:55.035595 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2024-05-01 01:24:55.118579 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2024-05-01 01:24:55.221017 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-05-01 01:24:55.29832 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-05-01 01:24:55.386767 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-05-01 01:24:55.4638 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-05-01 01:24:55.547765 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2024-05-01 01:24:55.624325 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-05-01 01:24:55.722701 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-05-01 01:24:55.812293 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-05-01 01:24:55.91213 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-05-01 01:24:56.007875 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2024-05-01 01:24:56.096337 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-05-01 01:24:56.205991 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-05-01 01:24:56.304179 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2024-05-01 01:24:56.401593 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2024-05-01 01:24:56.486329 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-05-01 01:24:56.582966 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2024-05-01 01:24:56.675096 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2024-05-01 01:24:56.769251 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-05-01 01:24:56.88066 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2024-05-01 01:24:56.97085 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2024-05-01 01:24:57.079128 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-05-01 01:24:57.172057 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2024-05-01 01:24:57.271068 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-05-01 01:24:57.365626 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-05-01 01:24:57.450627 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-05-01 01:24:57.552974 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-05-01 01:24:57.641847 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 4.4.0 alpha (2024-03-27 r86216)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.6.5
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] Maaslin2_1.18.0
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.4        biglm_0.9-2.1       xfun_0.43          
##  [4] bslib_0.6.2         ggplot2_3.5.0       lattice_0.22-6     
##  [7] numDeriv_2016.8-1.1 vctrs_0.6.5         tools_4.4.0        
## [10] generics_0.1.3      parallel_4.4.0      getopt_1.20.4      
## [13] tibble_3.2.1        fansi_1.0.6         DEoptimR_1.1-3     
## [16] cluster_2.1.6       pkgconfig_2.0.3     logging_0.10-108   
## [19] pheatmap_1.0.12     Matrix_1.7-0        data.table_1.15.4  
## [22] RColorBrewer_1.1-3  lifecycle_1.0.4     farver_2.1.1       
## [25] compiler_4.4.0      munsell_0.5.0       lmerTest_3.1-3     
## [28] permute_0.9-7       htmltools_0.5.8     sass_0.4.9         
## [31] hash_2.2.6.3        yaml_2.3.8          pillar_1.9.0       
## [34] nloptr_2.0.3        crayon_1.5.2        jquerylib_0.1.4    
## [37] MASS_7.3-60.2       cachem_1.0.8        vegan_2.6-4        
## [40] boot_1.3-30         nlme_3.1-164        robustbase_0.99-2  
## [43] tidyselect_1.2.1    digest_0.6.35       mvtnorm_1.2-4      
## [46] dplyr_1.1.4         labeling_0.4.3      splines_4.4.0      
## [49] pcaPP_2.0-4         fastmap_1.1.1       grid_4.4.0         
## [52] colorspace_2.1-0    cli_3.6.2           magrittr_2.0.3     
## [55] utf8_1.2.4          withr_3.0.0         scales_1.3.0       
## [58] rmarkdown_2.26      lme4_1.1-35.2       pbapply_1.7-2      
## [61] evaluate_0.23       knitr_1.45          mgcv_1.9-1         
## [64] rlang_1.1.3         Rcpp_1.0.12         glue_1.7.0         
## [67] optparse_1.7.4      DBI_1.2.2           minqa_1.2.6        
## [70] jsonlite_1.8.8      R6_2.5.1

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.