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"
## 2023-10-27 02:00:06.327459 INFO::Writing function arguments to log file
## 2023-10-27 02:00:06.353735 INFO::Verifying options selected are valid
## 2023-10-27 02:00:06.400306 INFO::Determining format of input files
## 2023-10-27 02:00:06.401954 INFO::Input format is data samples as rows and metadata samples as rows
## 2023-10-27 02:00:06.408403 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2023-10-27 02:00:06.409951 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2023-10-27 02:00:06.412382 INFO::Filter data based on min abundance and min prevalence
## 2023-10-27 02:00:06.413211 INFO::Total samples in data: 1595
## 2023-10-27 02:00:06.413907 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2023-10-27 02:00:06.419621 INFO::Total filtered features: 0
## 2023-10-27 02:00:06.420779 INFO::Filtered feature names from abundance and prevalence filtering:
## 2023-10-27 02:00:06.430861 INFO::Total filtered features with variance filtering: 0
## 2023-10-27 02:00:06.432064 INFO::Filtered feature names from variance filtering:
## 2023-10-27 02:00:06.432736 INFO::Running selected normalization method: TSS
## 2023-10-27 02:00:07.86307 INFO::Bypass z-score application to metadata
## 2023-10-27 02:00:07.864881 INFO::Running selected transform method: LOG
## 2023-10-27 02:00:07.905649 INFO::Running selected analysis method: LM
## 2023-10-27 02:00:08.648768 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:09.073136 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2023-10-27 02:00:09.271275 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2023-10-27 02:00:09.462261 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:09.6261 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2023-10-27 02:00:09.811195 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:09.988989 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2023-10-27 02:00:10.152603 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2023-10-27 02:00:10.329543 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2023-10-27 02:00:10.497909 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2023-10-27 02:00:10.711253 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:10.894016 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:11.068591 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:11.270128 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2023-10-27 02:00:11.440232 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:11.604858 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2023-10-27 02:00:11.787694 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2023-10-27 02:00:11.973101 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:12.138963 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:12.31219 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:12.500634 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:12.676138 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2023-10-27 02:00:12.843997 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2023-10-27 02:00:13.024305 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2023-10-27 02:00:13.198194 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2023-10-27 02:00:13.367348 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:13.545222 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2023-10-27 02:00:13.717927 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2023-10-27 02:00:13.891873 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:14.071184 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2023-10-27 02:00:14.248159 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2023-10-27 02:00:14.420121 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:14.604984 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:14.774117 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## Feature Alistipes.onderdonkii : simpleWarning: Model failed to converge with 1 negative eigenvalue: -6.2e+01
## 2023-10-27 02:00:14.923652 WARNING::Fitting problem for feature 34 a warning was issued
## boundary (singular) fit: see help('isSingular')
## Warning: Model failed to converge with 1 negative eigenvalue: -6.2e+01
## 2023-10-27 02:00:15.11663 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:15.290693 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2023-10-27 02:00:15.780315 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2023-10-27 02:00:15.942303 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2023-10-27 02:00:16.117796 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:16.295256 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:16.479985 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:16.64817 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:16.82008 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2023-10-27 02:00:17.099342 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2023-10-27 02:00:17.266934 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:17.4348 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:17.622603 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2023-10-27 02:00:17.792925 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2023-10-27 02:00:17.972435 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:18.163511 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:18.326142 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:18.494046 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:18.670449 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:18.842516 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2023-10-27 02:00:19.012767 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2023-10-27 02:00:19.194496 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2023-10-27 02:00:19.370583 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:19.557862 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:19.737524 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:19.91369 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:20.102215 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2023-10-27 02:00:20.270292 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:20.456666 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:20.622015 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2023-10-27 02:00:20.803529 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2023-10-27 02:00:20.977909 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2023-10-27 02:00:21.14683 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:21.314317 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2023-10-27 02:00:21.477526 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2023-10-27 02:00:21.656231 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:21.822008 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2023-10-27 02:00:21.989194 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2023-10-27 02:00:22.162143 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:22.354488 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2023-10-27 02:00:22.522127 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:22.691585 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:22.865563 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2023-10-27 02:00:23.02603 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2023-10-27 02:00:23.199827 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2023-10-27 02:00:23.380715 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2023-10-27 02:00:23.554893 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2023-10-27 02:00:23.740758 INFO::Fitting model to feature number 82, Escherichia.coli
## 2023-10-27 02:00:23.929851 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2023-10-27 02:00:24.089391 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:24.258448 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2023-10-27 02:00:24.444719 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2023-10-27 02:00:24.622843 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2023-10-27 02:00:24.864454 INFO::Counting total values for each feature
## 2023-10-27 02:00:24.903248 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2023-10-27 02:00:25.05159 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2023-10-27 02:00:25.222267 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2023-10-27 02:00:25.461195 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2023-10-27 02:00:25.550558 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2023-10-27 02:00:25.600455 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2023-10-27 02:00:25.609547 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2023-10-27 02:00:25.617892 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
## 2023-10-27 02:00:25.621721 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2023-10-27 02:00:25.911614 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2023-10-27 02:00:25.919888 INFO::Plotting associations from most to least significant, grouped by metadata
## 2023-10-27 02:00:25.92108 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2023-10-27 02:00:25.922938 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2023-10-27 02:00:26.327736 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2023-10-27 02:00:26.635607 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2023-10-27 02:00:26.919875 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2023-10-27 02:00:27.213982 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2023-10-27 02:00:27.496671 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2023-10-27 02:00:27.790283 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2023-10-27 02:00:28.082224 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2023-10-27 02:00:28.365168 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2023-10-27 02:00:28.660361 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2023-10-27 02:00:28.936587 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2023-10-27 02:00:29.224045 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2023-10-27 02:00:29.49338 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2023-10-27 02:00:29.770133 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2023-10-27 02:00:30.05401 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2023-10-27 02:00:30.322534 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2023-10-27 02:00:30.603747 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2023-10-27 02:00:30.876329 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2023-10-27 02:00:31.151653 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2023-10-27 02:00:31.4958 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-10-27 02:00:31.773042 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2023-10-27 02:00:32.075736 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2023-10-27 02:00:32.344803 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2023-10-27 02:00:32.616626 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2023-10-27 02:00:32.885049 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2023-10-27 02:00:33.17038 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2023-10-27 02:00:33.442629 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2023-10-27 02:00:33.729752 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2023-10-27 02:00:34.050057 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2023-10-27 02:00:34.324302 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2023-10-27 02:00:34.61301 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2023-10-27 02:00:34.885086 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2023-10-27 02:00:35.16474 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2023-10-27 02:00:35.416555 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2023-10-27 02:00:35.691497 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2023-10-27 02:00:35.963359 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2023-10-27 02:00:36.220074 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2023-10-27 02:00:36.497347 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2023-10-27 02:00:36.75898 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2023-10-27 02:00:37.03909 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2023-10-27 02:00:37.302955 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2023-10-27 02:00:37.599747 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2023-10-27 02:00:37.895016 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2023-10-27 02:00:38.170077 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2023-10-27 02:00:38.47038 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2023-10-27 02:00:38.749895 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2023-10-27 02:00:39.045961 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2023-10-27 02:00:39.346585 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2023-10-27 02:00:39.61417 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2023-10-27 02:00:39.92128 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2023-10-27 02:00:40.201906 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2023-10-27 02:00:40.471613 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2023-10-27 02:00:40.765536 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2023-10-27 02:00:41.03011 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2023-10-27 02:00:41.306792 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2023-10-27 02:00:41.583551 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2023-10-27 02:00:41.834303 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2023-10-27 02:00:42.175668 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2023-10-27 02:00:42.453894 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2023-10-27 02:00:42.72837 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2023-10-27 02:00:43.022666 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2023-10-27 02:00:43.311131 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2023-10-27 02:00:43.621142 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2023-10-27 02:00:47.50451 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2023-10-27 02:00:47.507072 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2023-10-27 02:00:47.74162 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2023-10-27 02:00:48.020535 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2023-10-27 02:00:48.324837 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2023-10-27 02:00:48.629261 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2023-10-27 02:00:48.913359 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2023-10-27 02:00:49.223328 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2023-10-27 02:00:49.494568 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2023-10-27 02:00:49.799166 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2023-10-27 02:00:50.087754 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2023-10-27 02:00:50.355823 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2023-10-27 02:00:50.661646 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2023-10-27 02:00:50.941559 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-10-27 02:00:51.241631 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2023-10-27 02:00:51.546428 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2023-10-27 02:00:51.826549 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2023-10-27 02:00:52.137539 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2023-10-27 02:00:52.437087 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2023-10-27 02:00:52.711643 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2023-10-27 02:00:53.001973 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2023-10-27 02:00:53.277543 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2023-10-27 02:00:53.991302 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2023-10-27 02:00:54.27684 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2023-10-27 02:00:54.544441 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2023-10-27 02:00:54.818985 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2023-10-27 02:00:55.076569 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2023-10-27 02:00:55.35157 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2023-10-27 02:00:55.602606 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2023-10-27 02:00:55.874321 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2023-10-27 02:00:56.130883 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2023-10-27 02:00:56.402535 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2023-10-27 02:00:56.698343 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2023-10-27 02:00:56.970604 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2023-10-27 02:00:57.251195 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2023-10-27 02:00:57.530299 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2023-10-27 02:00:57.801015 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2023-10-27 02:00:58.059096 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2023-10-27 02:00:58.336197 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2023-10-27 02:00:58.612594 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2023-10-27 02:00:58.885833 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2023-10-27 02:00:59.179495 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2023-10-27 02:00:59.457084 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2023-10-27 02:00:59.743174 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2023-10-27 02:01:00.006359 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2023-10-27 02:01:03.632373 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2023-10-27 02:01:03.634866 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2023-10-27 02:01:03.858383 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2023-10-27 02:01:04.159539 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2023-10-27 02:01:04.436944 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2023-10-27 02:01:04.711943 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2023-10-27 02:01:04.988683 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-10-27 02:01:05.287262 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2023-10-27 02:01:05.574446 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2023-10-27 02:01:05.845491 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2023-10-27 02:01:06.114212 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2023-10-27 02:01:06.390256 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2023-10-27 02:01:06.655598 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2023-10-27 02:01:06.95516 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2023-10-27 02:01:07.330921 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2023-10-27 02:01:07.618112 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2023-10-27 02:01:07.926136 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2023-10-27 02:01:08.190116 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2023-10-27 02:01:08.479918 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2023-10-27 02:01:08.77626 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2023-10-27 02:01:09.052785 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2023-10-27 02:01:09.345554 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2023-10-27 02:01:09.621341 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2023-10-27 02:01:09.925044 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2023-10-27 02:01:10.202531 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2023-10-27 02:01:10.489926 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2023-10-27 02:01:10.792894 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2023-10-27 02:01:11.064962 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2023-10-27 02:01:11.358966 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2023-10-27 02:01:11.633836 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2023-10-27 02:01:15.429503 INFO::Plotting data for metadata number 4, antibiotics
## 2023-10-27 02:01:15.432269 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2023-10-27 02:01:15.647252 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2023-10-27 02:01:15.94586 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2023-10-27 02:01:16.201107 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2023-10-27 02:01:16.490705 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2023-10-27 02:01:16.771046 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2023-10-27 02:01:17.030798 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2023-10-27 02:01:17.310787 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2023-10-27 02:01:17.574041 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2023-10-27 02:01:17.842457 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2023-10-27 02:01:18.244168 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2023-10-27 02:01:18.505141 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2023-10-27 02:01:18.802294 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2023-10-27 02:01:19.0727 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2023-10-27 02:01:19.36685 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2023-10-27 02:01:19.629312 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-10-27 02:01:19.926503 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2023-10-27 02:01:20.20642 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2023-10-27 02:01:20.479256 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2023-10-27 02:01:20.758573 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2023-10-27 02:01:21.024198 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2023-10-27 02:01:21.318561 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2023-10-27 02:01:21.579025 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2023-10-27 02:01:21.864731 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2023-10-27 02:01:22.12142 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2023-10-27 02:01:22.411081 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2023-10-27 02:01:22.690529 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2023-10-27 02:01:22.948418 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2023-10-27 02:01:23.23004 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2023-10-27 02:01:23.515203 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2023-10-27 02:01:23.810261 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2023-10-27 02:01:24.098173 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2023-10-27 02:01:24.340644 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2023-10-27 02:01:24.613663 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2023-10-27 02:01:24.874573 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2023-10-27 02:01:25.16207 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2023-10-27 02:01:25.439917 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2023-10-27 02:01:25.705823 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2023-10-27 02:01:26.001209 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2023-10-27 02:01:26.294102 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2023-10-27 02:01:30.051321 INFO::Plotting data for metadata number 5, age
## 2023-10-27 02:01:30.05452 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()`).
## 2023-10-27 02:01:30.393672 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()`).
## 2023-10-27 02:01:30.793956 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()`).
## 2023-10-27 02:01:31.101385 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()`).
## 2023-10-27 02:01:31.449969 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()`).
## 2023-10-27 02:01:31.717295 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()`).
## 2023-10-27 02:01:32.029904 INFO::Creating scatter plot for continuous data, age vs Clostridium.symbiosum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 20 rows containing missing values (`geom_point()`).
## 2023-10-27 02:01:32.36916 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()`).
## 2023-10-27 02:01:32.686097 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()`).
## 2023-10-27 02:01:32.958459 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()`).
## 2023-10-27 02:01:33.272772 INFO::Creating scatter plot for continuous data, age vs Veillonella.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 20 rows containing missing values (`geom_point()`).
## 2023-10-27 02:01:33.573811 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()`).
## 2023-10-27 02:01:33.879474 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()`).
## 2023-10-27 02:01:34.163346 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()`).
## 2023-10-27 02:01:34.455244 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()`).
## 2023-10-27 02:01:34.749759 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()`).
## 2023-10-27 02:01:35.055877 INFO::Creating scatter plot for continuous data, age vs Alistipes.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 20 rows containing missing values (`geom_point()`).
## 2023-10-27 02:01:35.356453 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()`).
## 2023-10-27 02:01:35.625282 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()`).
## 2023-10-27 02:01:35.936764 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()`).
## 2023-10-27 02:01:36.249719 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()`).
## 2023-10-27 02:01:36.549273 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 20 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()`).
## 2023-10-27 02:01:40.839684 INFO::Plotting data for metadata number 6, diagnosis
## 2023-10-27 02:01:40.842352 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2023-10-27 02:01:41.119867 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2023-10-27 02:01:41.412061 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2023-10-27 02:01:41.726416 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2023-10-27 02:01:42.059587 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2023-10-27 02:01:42.352937 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2023-10-27 02:01:42.684329 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2023-10-27 02:01:43.016939 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2023-10-27 02:01:43.291097 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2023-10-27 02:01:43.603514 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2023-10-27 02:01:43.932373 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2023-10-27 02:01:44.221537 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2023-10-27 02:01:44.564002 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2023-10-27 02:01:44.882124 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2023-10-27 02:01:45.161305 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2023-10-27 02:01:45.477211 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2023-10-27 02:01:45.788081 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2023-10-27 02:01:46.112697 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2023-10-27 02:01:46.42307 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2023-10-27 02:01:46.742947 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2023-10-27 02:01:47.051291 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2023-10-27 02:01:47.3293 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2023-10-27 02:01:47.665474 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2023-10-27 02:01:48.009233 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2023-10-27 02:01:48.724189 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2023-10-27 02:01:48.977823 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2023-10-27 02:01:49.23958 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2023-10-27 02:01:49.509085 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2023-10-27 02:01:49.78744 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2023-10-27 02:01:50.043033 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2023-10-27 02:01:50.320157 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2023-10-27 02:01:50.613633 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2023-10-27 02:01:50.877996 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2023-10-27 02:01:51.159466 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2023-10-27 02:01:51.426539 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2023-10-27 02:01:51.702937 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2023-10-27 02:01:51.961764 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2023-10-27 02:01:52.21987 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2023-10-27 02:01:52.495675 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2023-10-27 02:01:52.755942 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2023-10-27 02:01:53.026809 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2023-10-27 02:01:53.303418 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2023-10-27 02:01:53.568238 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 4.3.1 (2023-06-16)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.6.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] Maaslin2_1.16.0
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.3        biglm_0.9-2.1       xfun_0.39          
##  [4] bslib_0.5.0         ggplot2_3.4.2       lattice_0.21-8     
##  [7] numDeriv_2016.8-1.1 vctrs_0.6.3         tools_4.3.1        
## [10] generics_0.1.3      parallel_4.3.1      getopt_1.20.3      
## [13] tibble_3.2.1        fansi_1.0.4         DEoptimR_1.1-0     
## [16] cluster_2.1.4       pkgconfig_2.0.3     logging_0.10-108   
## [19] pheatmap_1.0.12     Matrix_1.6-0        data.table_1.14.8  
## [22] RColorBrewer_1.1-3  lifecycle_1.0.3     farver_2.1.1       
## [25] compiler_4.3.1      munsell_0.5.0       lmerTest_3.1-3     
## [28] permute_0.9-7       htmltools_0.5.5     sass_0.4.6         
## [31] hash_2.2.6.2        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         cachem_1.0.8        vegan_2.6-4        
## [40] boot_1.3-28.1       nlme_3.1-162        robustbase_0.99-0  
## [43] tidyselect_1.2.0    digest_0.6.33       mvtnorm_1.2-2      
## [46] dplyr_1.1.2         labeling_0.4.2      splines_4.3.1      
## [49] pcaPP_2.0-3         fastmap_1.1.1       grid_4.3.1         
## [52] colorspace_2.1-0    cli_3.6.1           magrittr_2.0.3     
## [55] utf8_1.2.3          withr_2.5.0         scales_1.2.1       
## [58] rmarkdown_2.23      lme4_1.1-34         pbapply_1.7-2      
## [61] evaluate_0.21       knitr_1.43          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_1.2.5        
## [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.