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"
## 2023-10-24 19:49:15.616781 INFO::Writing function arguments to log file
## 2023-10-24 19:49:15.640699 INFO::Verifying options selected are valid
## 2023-10-24 19:49:15.675477 INFO::Determining format of input files
## 2023-10-24 19:49:15.676633 INFO::Input format is data samples as rows and metadata samples as rows
## 2023-10-24 19:49:15.681578 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2023-10-24 19:49:15.689436 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2023-10-24 19:49:15.691696 INFO::Filter data based on min abundance and min prevalence
## 2023-10-24 19:49:15.692361 INFO::Total samples in data: 1595
## 2023-10-24 19:49:15.692979 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2023-10-24 19:49:15.696628 INFO::Total filtered features: 0
## 2023-10-24 19:49:15.697428 INFO::Filtered feature names from abundance and prevalence filtering:
## 2023-10-24 19:49:15.704786 INFO::Total filtered features with variance filtering: 0
## 2023-10-24 19:49:15.705581 INFO::Filtered feature names from variance filtering:
## 2023-10-24 19:49:15.706203 INFO::Running selected normalization method: TSS
## 2023-10-24 19:49:16.846214 INFO::Bypass z-score application to metadata
## 2023-10-24 19:49:16.847126 INFO::Running selected transform method: LOG
## 2023-10-24 19:49:16.865 INFO::Running selected analysis method: LM
## 2023-10-24 19:49:17.406662 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:17.725021 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2023-10-24 19:49:17.890131 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2023-10-24 19:49:18.041664 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:18.175576 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2023-10-24 19:49:18.324482 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:18.482662 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2023-10-24 19:49:18.61777 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2023-10-24 19:49:18.76423 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2023-10-24 19:49:18.90419 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2023-10-24 19:49:19.050913 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:19.191743 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:19.329772 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:19.482114 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2023-10-24 19:49:19.617936 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:19.749638 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2023-10-24 19:49:19.887048 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2023-10-24 19:49:20.029822 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:20.174397 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:20.316079 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:20.475331 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:20.619001 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2023-10-24 19:49:20.753281 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2023-10-24 19:49:20.896171 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2023-10-24 19:49:21.037277 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2023-10-24 19:49:21.172868 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:21.311744 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2023-10-24 19:49:21.451547 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2023-10-24 19:49:21.596364 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:21.742371 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2023-10-24 19:49:21.884479 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2023-10-24 19:49:22.025797 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:22.168433 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:22.304708 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:22.448512 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:22.585258 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2023-10-24 19:49:22.725951 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2023-10-24 19:49:22.863643 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2023-10-24 19:49:23.005774 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:23.155165 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:23.305463 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:23.449118 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:23.609268 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2023-10-24 19:49:23.761267 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2023-10-24 19:49:23.903666 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:24.040201 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:24.188256 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2023-10-24 19:49:24.324903 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2023-10-24 19:49:24.476105 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:24.624026 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:24.770092 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:24.910035 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:25.047949 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:25.189644 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2023-10-24 19:49:25.328383 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2023-10-24 19:49:25.468039 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2023-10-24 19:49:25.606481 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:25.752041 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:25.924154 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:26.067744 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:26.217404 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2023-10-24 19:49:26.584631 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:26.717623 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:26.851617 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2023-10-24 19:49:26.999336 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2023-10-24 19:49:27.142755 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2023-10-24 19:49:27.300564 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:27.442255 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2023-10-24 19:49:27.593737 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2023-10-24 19:49:27.735922 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:27.871716 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2023-10-24 19:49:28.005829 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2023-10-24 19:49:28.144981 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:28.276 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2023-10-24 19:49:28.418658 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:28.556237 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:28.686898 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2023-10-24 19:49:28.82554 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2023-10-24 19:49:28.960198 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2023-10-24 19:49:29.091309 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2023-10-24 19:49:29.234414 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2023-10-24 19:49:29.379721 INFO::Fitting model to feature number 82, Escherichia.coli
## 2023-10-24 19:49:29.527152 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2023-10-24 19:49:29.665236 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:29.801851 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2023-10-24 19:49:29.946986 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2023-10-24 19:49:30.087642 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2023-10-24 19:49:30.272271 INFO::Counting total values for each feature
## 2023-10-24 19:49:30.303128 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2023-10-24 19:49:30.447599 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2023-10-24 19:49:30.596698 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2023-10-24 19:49:30.830427 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2023-10-24 19:49:30.892032 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2023-10-24 19:49:30.92627 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2023-10-24 19:49:30.931556 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2023-10-24 19:49:30.937729 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
## 2023-10-24 19:49:30.940562 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2023-10-24 19:49:31.163113 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2023-10-24 19:49:31.168671 INFO::Plotting associations from most to least significant, grouped by metadata
## 2023-10-24 19:49:31.169538 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2023-10-24 19:49:31.170935 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2023-10-24 19:49:31.499876 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2023-10-24 19:49:31.740891 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2023-10-24 19:49:31.998213 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2023-10-24 19:49:32.235867 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2023-10-24 19:49:32.494891 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2023-10-24 19:49:32.750119 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2023-10-24 19:49:33.001749 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2023-10-24 19:49:33.248912 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2023-10-24 19:49:33.488697 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2023-10-24 19:49:33.770528 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2023-10-24 19:49:34.013911 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2023-10-24 19:49:34.260727 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2023-10-24 19:49:34.508377 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2023-10-24 19:49:34.746877 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2023-10-24 19:49:34.993733 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2023-10-24 19:49:35.229758 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2023-10-24 19:49:35.497249 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2023-10-24 19:49:35.745737 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2023-10-24 19:49:36.000205 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-10-24 19:49:36.270427 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2023-10-24 19:49:36.512923 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2023-10-24 19:49:36.764942 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2023-10-24 19:49:37.00127 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2023-10-24 19:49:37.253282 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2023-10-24 19:49:37.496398 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2023-10-24 19:49:37.754876 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2023-10-24 19:49:38.006135 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2023-10-24 19:49:38.269931 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2023-10-24 19:49:38.536381 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2023-10-24 19:49:38.781549 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2023-10-24 19:49:39.054879 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2023-10-24 19:49:39.315571 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2023-10-24 19:49:39.574972 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2023-10-24 19:49:39.824256 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2023-10-24 19:49:40.062387 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2023-10-24 19:49:40.306137 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2023-10-24 19:49:40.546017 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2023-10-24 19:49:40.79403 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2023-10-24 19:49:41.04672 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2023-10-24 19:49:41.284806 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2023-10-24 19:49:41.542382 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2023-10-24 19:49:41.790792 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2023-10-24 19:49:42.030067 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2023-10-24 19:49:42.282699 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2023-10-24 19:49:42.523009 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2023-10-24 19:49:42.781884 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2023-10-24 19:49:43.054202 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2023-10-24 19:49:43.295682 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2023-10-24 19:49:43.555128 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2023-10-24 19:49:43.849025 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2023-10-24 19:49:44.094075 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2023-10-24 19:49:44.351092 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2023-10-24 19:49:44.597623 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2023-10-24 19:49:44.848326 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2023-10-24 19:49:45.101571 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2023-10-24 19:49:45.33994 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2023-10-24 19:49:45.597318 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2023-10-24 19:49:45.833369 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2023-10-24 19:49:46.085764 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2023-10-24 19:49:46.330014 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2023-10-24 19:49:46.583373 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2023-10-24 19:49:46.832656 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2023-10-24 19:49:49.967041 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2023-10-24 19:49:49.969022 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2023-10-24 19:49:50.198581 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2023-10-24 19:49:50.449469 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2023-10-24 19:49:50.713372 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2023-10-24 19:49:50.973543 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2023-10-24 19:49:51.221292 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2023-10-24 19:49:51.483996 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2023-10-24 19:49:51.732777 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2023-10-24 19:49:51.9872 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2023-10-24 19:49:52.238694 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2023-10-24 19:49:52.488411 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2023-10-24 19:49:52.763938 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2023-10-24 19:49:53.025562 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-10-24 19:49:53.266994 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2023-10-24 19:49:53.525579 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2023-10-24 19:49:53.784521 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2023-10-24 19:49:54.030694 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2023-10-24 19:49:54.343641 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2023-10-24 19:49:54.593851 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2023-10-24 19:49:54.847168 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2023-10-24 19:49:55.105721 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2023-10-24 19:49:55.362366 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2023-10-24 19:49:55.869406 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2023-10-24 19:49:56.107501 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2023-10-24 19:49:56.34818 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2023-10-24 19:49:56.578522 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2023-10-24 19:49:56.820377 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2023-10-24 19:49:57.052455 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2023-10-24 19:49:57.28322 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2023-10-24 19:49:57.527775 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2023-10-24 19:49:57.761158 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2023-10-24 19:49:57.995018 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2023-10-24 19:49:58.236976 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2023-10-24 19:49:58.47843 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2023-10-24 19:49:58.733349 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2023-10-24 19:49:58.973519 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2023-10-24 19:49:59.232149 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2023-10-24 19:49:59.469933 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2023-10-24 19:49:59.708227 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2023-10-24 19:49:59.950327 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2023-10-24 19:50:00.183917 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2023-10-24 19:50:00.43098 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2023-10-24 19:50:00.668391 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2023-10-24 19:50:00.91376 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2023-10-24 19:50:03.821359 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2023-10-24 19:50:03.823105 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2023-10-24 19:50:04.034364 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2023-10-24 19:50:04.278501 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2023-10-24 19:50:04.517371 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2023-10-24 19:50:04.804731 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2023-10-24 19:50:05.05809 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-10-24 19:50:05.331028 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2023-10-24 19:50:05.586404 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2023-10-24 19:50:05.831506 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2023-10-24 19:50:06.079386 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2023-10-24 19:50:06.316842 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2023-10-24 19:50:06.568303 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2023-10-24 19:50:06.827637 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2023-10-24 19:50:07.099048 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2023-10-24 19:50:07.354895 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2023-10-24 19:50:07.599422 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2023-10-24 19:50:07.849487 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2023-10-24 19:50:08.090068 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2023-10-24 19:50:08.34682 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2023-10-24 19:50:08.594403 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2023-10-24 19:50:08.832584 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2023-10-24 19:50:09.089647 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2023-10-24 19:50:09.334146 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2023-10-24 19:50:09.58531 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2023-10-24 19:50:09.834663 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2023-10-24 19:50:10.080359 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2023-10-24 19:50:10.335126 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2023-10-24 19:50:10.579375 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2023-10-24 19:50:10.821528 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2023-10-24 19:50:13.898708 INFO::Plotting data for metadata number 4, antibiotics
## 2023-10-24 19:50:13.900667 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2023-10-24 19:50:14.105698 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2023-10-24 19:50:14.35143 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2023-10-24 19:50:14.583783 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2023-10-24 19:50:14.833301 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2023-10-24 19:50:15.067006 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2023-10-24 19:50:15.31194 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2023-10-24 19:50:15.560162 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2023-10-24 19:50:15.786976 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2023-10-24 19:50:16.035427 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2023-10-24 19:50:16.26903 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2023-10-24 19:50:16.508999 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2023-10-24 19:50:16.740829 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2023-10-24 19:50:16.993394 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2023-10-24 19:50:17.222626 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2023-10-24 19:50:17.464698 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-10-24 19:50:17.709698 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2023-10-24 19:50:17.940874 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2023-10-24 19:50:18.182053 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2023-10-24 19:50:18.405735 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2023-10-24 19:50:18.651299 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2023-10-24 19:50:18.895293 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2023-10-24 19:50:19.121646 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2023-10-24 19:50:19.37342 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2023-10-24 19:50:19.604393 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2023-10-24 19:50:19.852199 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2023-10-24 19:50:20.093563 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2023-10-24 19:50:20.326079 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2023-10-24 19:50:20.569145 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2023-10-24 19:50:20.823032 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2023-10-24 19:50:21.064571 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2023-10-24 19:50:21.312388 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2023-10-24 19:50:21.564091 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2023-10-24 19:50:21.824696 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2023-10-24 19:50:22.079928 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2023-10-24 19:50:22.309841 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2023-10-24 19:50:22.616703 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2023-10-24 19:50:22.864774 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2023-10-24 19:50:23.108423 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2023-10-24 19:50:23.362857 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2023-10-24 19:50:26.306 INFO::Plotting data for metadata number 5, age
## 2023-10-24 19:50:26.307821 INFO::Creating scatter plot for continuous data, age vs Haemophilus.parainfluenzae
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:26.612116 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.pseudocatenulatum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:26.954771 INFO::Creating scatter plot for continuous data, age vs Faecalibacterium.prausnitzii
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:27.212226 INFO::Creating scatter plot for continuous data, age vs Clostridium.clostridioforme
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:27.468646 INFO::Creating scatter plot for continuous data, age vs Veillonella.parvula
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:27.732809 INFO::Creating scatter plot for continuous data, age vs Subdoligranulum.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:28.004717 INFO::Creating scatter plot for continuous data, age vs Clostridium.symbiosum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:28.28383 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.gnavus
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:28.527614 INFO::Creating scatter plot for continuous data, age vs Dialister.invisus
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:28.792354 INFO::Creating scatter plot for continuous data, age vs Veillonella.dispar
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:29.056307 INFO::Creating scatter plot for continuous data, age vs Veillonella.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:29.318982 INFO::Creating scatter plot for continuous data, age vs Bacteroides.thetaiotaomicron
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:29.583983 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.bromii
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:29.844795 INFO::Creating scatter plot for continuous data, age vs Bacteroides.intestinalis
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:30.105419 INFO::Creating scatter plot for continuous data, age vs Eubacterium.siraeum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:30.36806 INFO::Creating scatter plot for continuous data, age vs Prevotella.copri
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:30.625492 INFO::Creating scatter plot for continuous data, age vs Alistipes.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:30.918686 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 (`geom_point()`).
## 2023-10-24 19:50:31.168777 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.longum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:31.427955 INFO::Creating scatter plot for continuous data, age vs Akkermansia.muciniphila
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:31.696759 INFO::Creating scatter plot for continuous data, age vs Collinsella.aerofaciens
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:31.95985 INFO::Creating scatter plot for continuous data, age vs Parabacteroides.distasonis
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-10-24 19:50:35.241668 INFO::Plotting data for metadata number 6, diagnosis
## 2023-10-24 19:50:35.24367 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2023-10-24 19:50:35.495293 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2023-10-24 19:50:35.743372 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2023-10-24 19:50:36.017124 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2023-10-24 19:50:36.305498 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2023-10-24 19:50:36.551649 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2023-10-24 19:50:36.819629 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2023-10-24 19:50:37.089744 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2023-10-24 19:50:37.35673 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2023-10-24 19:50:37.613815 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2023-10-24 19:50:37.885201 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2023-10-24 19:50:38.158265 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2023-10-24 19:50:38.410945 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2023-10-24 19:50:38.679665 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2023-10-24 19:50:38.944785 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2023-10-24 19:50:39.258064 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2023-10-24 19:50:39.505733 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2023-10-24 19:50:39.78421 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2023-10-24 19:50:40.053905 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2023-10-24 19:50:40.31714 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2023-10-24 19:50:40.585338 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2023-10-24 19:50:40.847813 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2023-10-24 19:50:41.104991 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2023-10-24 19:50:41.37758 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2023-10-24 19:50:41.638867 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2023-10-24 19:50:41.900315 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2023-10-24 19:50:42.170371 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2023-10-24 19:50:42.444532 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2023-10-24 19:50:42.718573 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2023-10-24 19:50:43.008514 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2023-10-24 19:50:43.298414 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2023-10-24 19:50:43.545513 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2023-10-24 19:50:43.818168 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2023-10-24 19:50:44.101073 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2023-10-24 19:50:44.368014 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2023-10-24 19:50:44.630656 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2023-10-24 19:50:44.904633 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2023-10-24 19:50:45.181802 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2023-10-24 19:50:45.459505 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2023-10-24 19:50:45.722151 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2023-10-24 19:50:46.000468 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2023-10-24 19:50:46.284077 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2023-10-24 19:50:46.55292 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 Under development (unstable) (2023-10-22 r85388)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [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_1.17.0
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.4        biglm_0.9-2.1       xfun_0.40          
##  [4] bslib_0.5.1         ggplot2_3.4.4       lattice_0.22-5     
##  [7] numDeriv_2016.8-1.1 vctrs_0.6.4         tools_4.4.0        
## [10] generics_0.1.3      parallel_4.4.0      getopt_1.20.4      
## [13] tibble_3.2.1        fansi_1.0.5         DEoptimR_1.1-3     
## [16] cluster_2.1.4       pkgconfig_2.0.3     logging_0.10-108   
## [19] pheatmap_1.0.12     Matrix_1.6-1.1      data.table_1.14.8  
## [22] RColorBrewer_1.1-3  lifecycle_1.0.3     farver_2.1.1       
## [25] compiler_4.4.0      munsell_0.5.0       lmerTest_3.1-3     
## [28] permute_0.9-7       htmltools_0.5.6.1   sass_0.4.7         
## [31] hash_2.2.6.3        yaml_2.3.7          pillar_1.9.0       
## [34] nloptr_2.0.3        crayon_1.5.2        jquerylib_0.1.4    
## [37] MASS_7.3-60.1       cachem_1.0.8        vegan_2.6-4        
## [40] boot_1.3-28.1       nlme_3.1-163        robustbase_0.99-0  
## [43] tidyselect_1.2.0    digest_0.6.33       mvtnorm_1.2-3      
## [46] dplyr_1.1.3         labeling_0.4.3      splines_4.4.0      
## [49] pcaPP_2.0-3         fastmap_1.1.1       grid_4.4.0         
## [52] colorspace_2.1-0    cli_3.6.1           magrittr_2.0.3     
## [55] utf8_1.2.4          withr_2.5.1         scales_1.2.1       
## [58] rmarkdown_2.25      lme4_1.1-34         pbapply_1.7-2      
## [61] evaluate_0.22       knitr_1.44          mgcv_1.9-0         
## [64] rlang_1.1.1         Rcpp_1.0.11         glue_1.6.2         
## [67] optparse_1.7.3      DBI_1.1.3           minqa_1.2.6        
## [70] jsonlite_1.8.7      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.