MaAsLin2 User Manual

MaAsLin2 is the next generation of MaAsLin (Microbiome Multivariable Association with Linear Models).

MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta-omics features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, along with a variety of filtering, normalization, and transform methods.

If you use the MaAsLin2 software, please cite our manuscript:

Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C (2021). Multivariable Association Discovery in Population-scale Meta-omics Studies. PLoS Computational Biology, 17(11):e1009442.

Check out the MaAsLin 2 tutorial for an overview of analysis options.

If you have questions, please direct it to :
MaAsLin2 Forum
Google Groups (Read only)


Description

MaAsLin2 finds associations between microbiome multi-omics features and complex metadata in population-scale epidemiological studies. The software includes multiple analysis methods (with support for multiple covariates and repeated measures), filtering, normalization, and transform options to customize analysis for your specific study.

Requirements

MaAsLin2 is an R package that can be run on the command line or as an R function.

Installation

MaAsLin2 can be run from the command line or as an R function. If only running from the command line, you do not need to install the MaAsLin2 package but you will need to install the MaAsLin2 dependencies.

From command line

  1. Download the source: MaAsLin2.tar.gz
  2. Decompress the download:
    • $ tar xzvf maaslin2.tar.gz
  3. Install the Bioconductor dependencies edgeR and metagenomeSeq.
  4. Install the CRAN dependencies:
    • $ R -q -e "install.packages(c('lmerTest','pbapply','car','dplyr','vegan','chemometrics','ggplot2','pheatmap','hash','logging','data.table','glmmTMB','MASS','cplm','pscl'), repos='http://cran.r-project.org')"
  5. Install the MaAsLin2 package (only r,equired if running as an R function):
    • $ R CMD INSTALL maaslin2

From R

Install Bioconductor and then install Maaslin2

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Maaslin2")

How to Run

MaAsLin2 can be run from the command line or as an R function. Both methods require the same arguments, have the same options, and use the same default settings.

Input Files

MaAsLin2 requires two input files.

  1. Data (or features) file
    • This file is tab-delimited.
    • Formatted with features as columns and samples as rows.
    • The transpose of this format is also okay.
    • Possible features in this file include taxonomy or genes.
  2. Metadata file
    • This file is tab-delimited.
    • Formatted with features as columns and samples as rows.
    • The transpose of this format is also okay.
    • Possible metadata in this file include gender or age.

The data file can contain samples not included in the metadata file (along with the reverse case). For both cases, those samples not included in both files will be removed from the analysis. Also the samples do not need to be in the same order in the two files.

NOTE: If running MaAsLin2 as a function, the data and metadata inputs can be of type data.frame instead of a path to a file.

Output Files

MaAsLin2 generates two types of output files: data and visualization.

  1. Data output files
    • all_results.tsv
      • This includes the same data as the data.frame returned.
      • This file contains all results ordered by increasing q-value.
      • The first columns are the metadata and feature names.
      • The next two columns are the value and coefficient from the model.
      • The next column is the standard deviation from the model.
      • The N column is the total number of data points.
      • The N.not.zero column is the total of non-zero data points.
      • The pvalue from the calculation is the second to last column.
      • The qvalue is computed with p.adjust with the correction method.
    • significant_results.tsv
      • This file is a subset of the results in the first file.
      • It only includes associations with q-values <= to the threshold.
    • ``features```
      • This folder includes the filtered, normalized, and transformed versions of the input feature table.
      • These steps are performed sequentially in the above order.
      • If an option is set such that a step does not change the data, the resulting table will still be output.
    • models.rds
      • This file contains a list with every model fit object.
      • It will only be generated if save_models is set to TRUE.
    • residuals.rds
      • This file contains a data frame with residuals for each feature.
    • fitted.rds
      • This file contains a data frame with fitted values for each feature.
    • ranef.rds
      • This file contains a data frame with extracted random effects for each feature (when random effects are specified).
    • maaslin2.log
      • This file contains all log information for the run.
      • It includes all settings, warnings, errors, and steps run.
  2. Visualization output files
    • heatmap.pdf
      • This file contains a heatmap of the significant associations.
    • [a-z/0-9]+.pdf
      • A plot is generated for each significant association.
      • Scatter plots are used for continuous metadata.
      • Box plots are for categorical data.
      • Data points plotted are after filtering but prior to normalization and transform.

Run a Demo

Example input files can be found in the inst/extdata folder of the MaAsLin2 source. The files provided were generated from the HMP2 data which can be downloaded from https://ibdmdb.org/ .

HMP2_taxonomy.tsv: is a tab-demilited file with species as columns and samples as rows. It is a subset of the taxonomy file so it just includes the species abundances for all samples.

HMP2_metadata.tsv: is a tab-delimited file with samples as rows and metadata as columns. It is a subset of the metadata file so that it just includes some of the fields.

Command line

$ Maaslin2.R --fixed_effects="diagnosis,dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age" --random_effects="site,subject" --standardize=FALSE inst/extdata/HMP2_taxonomy.tsv inst/extdata/HMP2_metadata.tsv demo_output

  • Make sure to provide the full path to the MaAsLin2 executable (ie ./R/Maaslin2.R).
  • In the demo command:
    • HMP2_taxonomy.tsv is the path to your data (or features) file
    • HMP2_metadata.tsv is the path to your metadata file
    • demo_output is the path to the folder to write the output

In R

library(Maaslin2)
input_data <- system.file(
    'extdata','HMP2_taxonomy.tsv', package="Maaslin2")
input_metadata <-system.file(
    'extdata','HMP2_metadata.tsv', package="Maaslin2")
fit_data <- Maaslin2(
    input_data, input_metadata, 'demo_output',
    fixed_effects = c('diagnosis', 'dysbiosisnonIBD','dysbiosisUC','dysbiosisCD', 'antibiotics', 'age'),
    random_effects = c('site', 'subject'),
    reference = "diagnosis,nonIBD",
    standardize = FALSE)
## [1] "Creating output folder"
## [1] "Creating output feature tables folder"
## [1] "Creating output fits folder"
## [1] "Creating output figures folder"
## 2024-12-18 16:49:32.798951 INFO::Writing function arguments to log file
## 2024-12-18 16:49:32.807576 INFO::Verifying options selected are valid
## 2024-12-18 16:49:32.821297 INFO::Determining format of input files
## 2024-12-18 16:49:32.82181 INFO::Input format is data samples as rows and metadata samples as rows
## 2024-12-18 16:49:32.823932 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2024-12-18 16:49:32.824335 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2024-12-18 16:49:32.825107 INFO::Filter data based on min abundance and min prevalence
## 2024-12-18 16:49:32.825364 INFO::Total samples in data: 1595
## 2024-12-18 16:49:32.825595 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2024-12-18 16:49:32.827254 INFO::Total filtered features: 0
## 2024-12-18 16:49:32.827594 INFO::Filtered feature names from abundance and prevalence filtering:
## 2024-12-18 16:49:32.830637 INFO::Total filtered features with variance filtering: 0
## 2024-12-18 16:49:32.83117 INFO::Filtered feature names from variance filtering:
## 2024-12-18 16:49:32.831486 INFO::Running selected normalization method: TSS
## 2024-12-18 16:49:33.255677 INFO::Bypass z-score application to metadata
## 2024-12-18 16:49:33.256151 INFO::Running selected transform method: LOG
## 2024-12-18 16:49:33.361247 INFO::Running selected analysis method: LM
## 2024-12-18 16:49:33.467485 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:33.592883 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2024-12-18 16:49:33.649093 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2024-12-18 16:49:33.714434 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:33.764591 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2024-12-18 16:49:33.915166 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:33.964212 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2024-12-18 16:49:34.012633 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2024-12-18 16:49:34.066752 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2024-12-18 16:49:34.116067 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2024-12-18 16:49:34.162639 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:34.21245 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:34.269154 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:34.324108 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2024-12-18 16:49:34.376475 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:34.436678 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2024-12-18 16:49:34.490668 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2024-12-18 16:49:34.544975 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:34.59761 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:34.654031 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:34.704177 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:34.755455 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2024-12-18 16:49:34.809396 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2024-12-18 16:49:34.861134 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2024-12-18 16:49:34.914822 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2024-12-18 16:49:34.970944 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:35.021667 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2024-12-18 16:49:35.074497 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2024-12-18 16:49:35.127205 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## Feature Parabacteroides.unclassified : simpleWarning: Model failed to converge with 1 negative eigenvalue: -3.4e+01
## 2024-12-18 16:49:35.17398 WARNING::Fitting problem for feature 29 a warning was issued
## boundary (singular) fit: see help('isSingular')
## Warning: Model failed to converge with 1 negative eigenvalue: -3.4e+01
## 2024-12-18 16:49:35.225209 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2024-12-18 16:49:35.278765 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2024-12-18 16:49:35.334775 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:35.386741 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:35.437836 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:35.499674 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:35.55276 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2024-12-18 16:49:35.606669 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2024-12-18 16:49:35.767172 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2024-12-18 16:49:35.818415 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:35.870674 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:35.923156 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:35.971759 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.020227 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2024-12-18 16:49:36.075014 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2024-12-18 16:49:36.128485 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.177476 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.227753 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2024-12-18 16:49:36.278108 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2024-12-18 16:49:36.328246 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.381028 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.431779 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.478781 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.525001 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.576123 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2024-12-18 16:49:36.623817 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2024-12-18 16:49:36.672238 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2024-12-18 16:49:36.72612 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.774135 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.821713 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.878969 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:36.932971 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2024-12-18 16:49:36.9835 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:37.034315 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:37.089711 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2024-12-18 16:49:37.152915 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2024-12-18 16:49:37.2065 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2024-12-18 16:49:37.264947 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:37.316135 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2024-12-18 16:49:37.36717 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2024-12-18 16:49:37.425409 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:37.480604 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2024-12-18 16:49:37.536695 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2024-12-18 16:49:37.592705 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:37.648746 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2024-12-18 16:49:37.700587 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:37.756254 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:37.805478 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2024-12-18 16:49:37.857896 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2024-12-18 16:49:37.909052 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2024-12-18 16:49:38.066281 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2024-12-18 16:49:38.117883 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2024-12-18 16:49:38.171127 INFO::Fitting model to feature number 82, Escherichia.coli
## 2024-12-18 16:49:38.225595 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2024-12-18 16:49:38.272295 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:38.320579 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2024-12-18 16:49:38.375294 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2024-12-18 16:49:38.427115 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2024-12-18 16:49:38.492788 INFO::Counting total values for each feature
## 2024-12-18 16:49:38.509844 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2024-12-18 16:49:38.559382 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2024-12-18 16:49:38.618697 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2024-12-18 16:49:38.702925 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2024-12-18 16:49:38.733329 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2024-12-18 16:49:38.750409 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2024-12-18 16:49:38.753344 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2024-12-18 16:49:38.756068 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): demo_output/significant_results.tsv
## 2024-12-18 16:49:38.757317 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2024-12-18 16:49:38.816307 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2024-12-18 16:49:38.819054 INFO::Plotting associations from most to least significant, grouped by metadata
## 2024-12-18 16:49:38.819432 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2024-12-18 16:49:38.820155 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2024-12-18 16:49:38.947326 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2024-12-18 16:49:39.056814 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2024-12-18 16:49:39.144931 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2024-12-18 16:49:39.236493 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2024-12-18 16:49:39.322019 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2024-12-18 16:49:39.412104 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2024-12-18 16:49:39.497053 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2024-12-18 16:49:39.587912 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2024-12-18 16:49:39.675754 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2024-12-18 16:49:39.764784 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2024-12-18 16:49:39.849775 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2024-12-18 16:49:39.939059 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2024-12-18 16:49:40.021908 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2024-12-18 16:49:40.112383 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2024-12-18 16:49:40.197298 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2024-12-18 16:49:40.291609 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2024-12-18 16:49:40.383645 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2024-12-18 16:49:40.47441 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2024-12-18 16:49:40.563444 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-12-18 16:49:40.654432 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2024-12-18 16:49:40.742435 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2024-12-18 16:49:40.834816 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2024-12-18 16:49:40.948234 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2024-12-18 16:49:41.03398 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2024-12-18 16:49:41.124589 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2024-12-18 16:49:41.209527 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2024-12-18 16:49:41.312024 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2024-12-18 16:49:41.397061 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2024-12-18 16:49:41.491619 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2024-12-18 16:49:41.574409 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2024-12-18 16:49:41.663597 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2024-12-18 16:49:41.74508 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2024-12-18 16:49:41.827596 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2024-12-18 16:49:41.910436 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2024-12-18 16:49:42.008174 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2024-12-18 16:49:42.089 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2024-12-18 16:49:42.182554 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2024-12-18 16:49:42.267176 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2024-12-18 16:49:42.358874 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2024-12-18 16:49:42.441822 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2024-12-18 16:49:42.533839 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2024-12-18 16:49:42.616334 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2024-12-18 16:49:42.701153 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2024-12-18 16:49:42.783284 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2024-12-18 16:49:42.873068 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2024-12-18 16:49:42.955025 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2024-12-18 16:49:43.045128 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2024-12-18 16:49:43.131646 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2024-12-18 16:49:43.226022 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2024-12-18 16:49:43.319873 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2024-12-18 16:49:43.399271 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2024-12-18 16:49:43.489178 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2024-12-18 16:49:43.572715 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2024-12-18 16:49:43.65692 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2024-12-18 16:49:43.737209 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2024-12-18 16:49:43.819792 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2024-12-18 16:49:43.893006 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2024-12-18 16:49:43.974941 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2024-12-18 16:49:44.063097 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2024-12-18 16:49:44.154927 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2024-12-18 16:49:44.254694 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2024-12-18 16:49:44.339512 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-12-18 16:49:45.224679 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2024-12-18 16:49:45.225505 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2024-12-18 16:49:45.289278 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2024-12-18 16:49:45.408101 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2024-12-18 16:49:45.499224 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2024-12-18 16:49:45.589655 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2024-12-18 16:49:45.671418 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2024-12-18 16:49:45.76392 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2024-12-18 16:49:45.845515 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2024-12-18 16:49:45.943901 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2024-12-18 16:49:46.040714 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2024-12-18 16:49:46.143498 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2024-12-18 16:49:46.237444 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2024-12-18 16:49:46.337079 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-12-18 16:49:46.431705 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2024-12-18 16:49:46.527018 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2024-12-18 16:49:46.626697 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2024-12-18 16:49:46.715992 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2024-12-18 16:49:46.81144 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2024-12-18 16:49:46.898907 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2024-12-18 16:49:46.989667 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2024-12-18 16:49:47.074854 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2024-12-18 16:49:47.169064 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2024-12-18 16:49:47.253034 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2024-12-18 16:49:47.34466 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2024-12-18 16:49:47.427995 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2024-12-18 16:49:47.512407 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2024-12-18 16:49:47.598654 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2024-12-18 16:49:47.677807 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2024-12-18 16:49:47.764493 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2024-12-18 16:49:47.846325 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2024-12-18 16:49:47.935546 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2024-12-18 16:49:48.01629 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2024-12-18 16:49:48.112157 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2024-12-18 16:49:48.194527 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2024-12-18 16:49:48.290338 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2024-12-18 16:49:48.379429 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2024-12-18 16:49:48.466885 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2024-12-18 16:49:48.557581 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2024-12-18 16:49:48.6409 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2024-12-18 16:49:48.734264 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2024-12-18 16:49:48.821143 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2024-12-18 16:49:48.953085 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2024-12-18 16:49:49.054518 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2024-12-18 16:49:49.145544 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2024-12-18 16:49:50.133855 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2024-12-18 16:49:50.13465 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2024-12-18 16:49:50.205222 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2024-12-18 16:49:50.290349 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2024-12-18 16:49:50.38067 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2024-12-18 16:49:50.458052 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2024-12-18 16:49:50.547051 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-12-18 16:49:50.637377 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2024-12-18 16:49:50.725906 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2024-12-18 16:49:50.811024 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2024-12-18 16:49:50.897953 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2024-12-18 16:49:50.979681 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2024-12-18 16:49:51.070476 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2024-12-18 16:49:51.156515 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2024-12-18 16:49:51.244509 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2024-12-18 16:49:51.329564 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2024-12-18 16:49:51.41692 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2024-12-18 16:49:51.494773 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2024-12-18 16:49:51.578325 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2024-12-18 16:49:51.667341 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2024-12-18 16:49:51.74713 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2024-12-18 16:49:51.831197 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2024-12-18 16:49:51.913637 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2024-12-18 16:49:52.004352 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2024-12-18 16:49:52.087663 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2024-12-18 16:49:52.172932 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2024-12-18 16:49:52.257252 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2024-12-18 16:49:52.347712 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2024-12-18 16:49:52.42862 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2024-12-18 16:49:52.516491 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2024-12-18 16:49:53.402365 INFO::Plotting data for metadata number 4, antibiotics
## 2024-12-18 16:49:53.403248 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2024-12-18 16:49:53.474745 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2024-12-18 16:49:53.557645 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2024-12-18 16:49:53.646388 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2024-12-18 16:49:53.727775 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2024-12-18 16:49:53.812077 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2024-12-18 16:49:53.892429 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2024-12-18 16:49:53.980563 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2024-12-18 16:49:54.056059 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2024-12-18 16:49:54.141627 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2024-12-18 16:49:54.228682 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2024-12-18 16:49:54.317713 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2024-12-18 16:49:54.396872 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2024-12-18 16:49:54.484632 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2024-12-18 16:49:54.564637 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2024-12-18 16:49:54.650972 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-12-18 16:49:54.730103 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2024-12-18 16:49:54.82024 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2024-12-18 16:49:54.898911 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2024-12-18 16:49:54.980885 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2024-12-18 16:49:55.061186 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2024-12-18 16:49:55.146851 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2024-12-18 16:49:55.223682 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2024-12-18 16:49:55.313487 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2024-12-18 16:49:55.392903 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2024-12-18 16:49:55.481038 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2024-12-18 16:49:55.558162 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2024-12-18 16:49:55.647656 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2024-12-18 16:49:55.724914 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2024-12-18 16:49:55.819802 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2024-12-18 16:49:55.899044 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2024-12-18 16:49:55.986622 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2024-12-18 16:49:56.068184 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2024-12-18 16:49:56.1526 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2024-12-18 16:49:56.229344 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2024-12-18 16:49:56.335685 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2024-12-18 16:49:56.411493 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-12-18 16:49:56.521188 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2024-12-18 16:49:56.604904 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2024-12-18 16:49:56.694401 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2024-12-18 16:49:57.560877 INFO::Plotting data for metadata number 5, age
## 2024-12-18 16:49:57.561718 INFO::Creating scatter plot for continuous data, age vs Haemophilus.parainfluenzae
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:57.647375 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.pseudocatenulatum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:57.765085 INFO::Creating scatter plot for continuous data, age vs Faecalibacterium.prausnitzii
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:57.849311 INFO::Creating scatter plot for continuous data, age vs Clostridium.clostridioforme
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:57.930539 INFO::Creating scatter plot for continuous data, age vs Veillonella.parvula
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.014506 INFO::Creating scatter plot for continuous data, age vs Subdoligranulum.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.100454 INFO::Creating scatter plot for continuous data, age vs Clostridium.symbiosum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.182188 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.gnavus
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.26575 INFO::Creating scatter plot for continuous data, age vs Dialister.invisus
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.340127 INFO::Creating scatter plot for continuous data, age vs Veillonella.dispar
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.422563 INFO::Creating scatter plot for continuous data, age vs Veillonella.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.502628 INFO::Creating scatter plot for continuous data, age vs Bacteroides.thetaiotaomicron
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.575299 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.bromii
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.660007 INFO::Creating scatter plot for continuous data, age vs Bacteroides.intestinalis
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.738612 INFO::Creating scatter plot for continuous data, age vs Eubacterium.siraeum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.805017 INFO::Creating scatter plot for continuous data, age vs Prevotella.copri
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.884553 INFO::Creating scatter plot for continuous data, age vs Alistipes.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:58.958332 INFO::Creating scatter plot for continuous data, age vs Bacteroidales.bacterium.ph8
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:59.027149 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.longum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:59.109939 INFO::Creating scatter plot for continuous data, age vs Akkermansia.muciniphila
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:59.190716 INFO::Creating scatter plot for continuous data, age vs Collinsella.aerofaciens
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:49:59.274894 INFO::Creating scatter plot for continuous data, age vs Parabacteroides.distasonis
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2024-12-18 16:50:00.258955 INFO::Plotting data for metadata number 6, diagnosis
## 2024-12-18 16:50:00.259747 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2024-12-18 16:50:00.340566 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-12-18 16:50:00.430292 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-12-18 16:50:00.52885 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-12-18 16:50:00.615899 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-12-18 16:50:00.712843 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2024-12-18 16:50:00.795693 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-12-18 16:50:00.889393 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-12-18 16:50:00.980843 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-12-18 16:50:01.07242 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-12-18 16:50:01.167109 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2024-12-18 16:50:01.253851 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-12-18 16:50:01.353363 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-12-18 16:50:01.438363 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-12-18 16:50:01.535112 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2024-12-18 16:50:01.630432 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2024-12-18 16:50:01.724211 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-12-18 16:50:01.82225 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-12-18 16:50:01.908412 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-12-18 16:50:02.009889 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-12-18 16:50:02.100068 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2024-12-18 16:50:02.194825 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-12-18 16:50:02.290505 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-12-18 16:50:02.378097 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-12-18 16:50:02.475005 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-12-18 16:50:02.567526 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2024-12-18 16:50:02.655556 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-12-18 16:50:02.780727 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-12-18 16:50:02.866373 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2024-12-18 16:50:02.969202 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2024-12-18 16:50:03.05505 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-12-18 16:50:03.160081 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2024-12-18 16:50:03.252787 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2024-12-18 16:50:03.352602 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-12-18 16:50:03.455857 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2024-12-18 16:50:03.544093 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2024-12-18 16:50:03.64689 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-12-18 16:50:03.736075 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2024-12-18 16:50:03.845554 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-12-18 16:50:03.932915 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-12-18 16:50:04.035207 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-12-18 16:50:04.139825 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-12-18 16:50:04.227696 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) (2024-11-20 r87352)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
## 
## 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_1.21.0
## 
## loaded via a namespace (and not attached):
##  [1] sass_0.4.9          generics_0.1.3      robustbase_0.99-4-1
##  [4] lattice_0.22-6      lme4_1.1-35.5       digest_0.6.37      
##  [7] magrittr_2.0.3      RColorBrewer_1.1-3  evaluate_1.0.1     
## [10] grid_4.5.0          mvtnorm_1.3-2       fastmap_1.2.0      
## [13] jsonlite_1.8.9      Matrix_1.7-1        DBI_1.2.3          
## [16] optparse_1.7.5      biglm_0.9-3         mgcv_1.9-1         
## [19] scales_1.3.0        pbapply_1.7-2       permute_0.9-7      
## [22] numDeriv_2016.8-1.1 getopt_1.20.4       jquerylib_0.1.4    
## [25] cli_3.6.3           rlang_1.1.4         crayon_1.5.3       
## [28] munsell_0.5.1       splines_4.5.0       withr_3.0.2        
## [31] cachem_1.1.0        yaml_2.3.10         vegan_2.6-8        
## [34] tools_4.5.0         parallel_4.5.0      nloptr_2.1.1       
## [37] minqa_1.2.8         dplyr_1.1.4         colorspace_2.1-1   
## [40] ggplot2_3.5.1       boot_1.3-31         hash_2.2.6.3       
## [43] vctrs_0.6.5         R6_2.5.1            lifecycle_1.0.4    
## [46] MASS_7.3-61         logging_0.10-108    pcaPP_2.0-5        
## [49] cluster_2.1.8       pkgconfig_2.0.3     gtable_0.3.6       
## [52] lmerTest_3.1-3      pillar_1.10.0       bslib_0.8.0        
## [55] Rcpp_1.0.13-1       data.table_1.16.4   glue_1.8.0         
## [58] DEoptimR_1.1-3-1    xfun_0.49           tibble_3.2.1       
## [61] tidyselect_1.2.1    knitr_1.49          farver_2.1.2       
## [64] htmltools_0.5.8.1   nlme_3.1-166        labeling_0.4.3     
## [67] rmarkdown_2.29      pheatmap_1.0.12     compiler_4.5.0

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.