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"
## 2023-06-12 11:36:13.081708 INFO::Writing function arguments to log file
## 2023-06-12 11:36:13.135266 INFO::Verifying options selected are valid
## 2023-06-12 11:36:13.200952 INFO::Determining format of input files
## 2023-06-12 11:36:13.202697 INFO::Input format is data samples as rows and metadata samples as rows
## 2023-06-12 11:36:13.211316 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2023-06-12 11:36:13.213121 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2023-06-12 11:36:13.218319 INFO::Filter data based on min abundance and min prevalence
## 2023-06-12 11:36:13.219558 INFO::Total samples in data: 1595
## 2023-06-12 11:36:13.222481 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2023-06-12 11:36:13.22855 INFO::Total filtered features: 0
## 2023-06-12 11:36:13.229956 INFO::Filtered feature names from abundance and prevalence filtering:
## 2023-06-12 11:36:13.244967 INFO::Total filtered features with variance filtering: 0
## 2023-06-12 11:36:13.246431 INFO::Filtered feature names from variance filtering:
## 2023-06-12 11:36:13.247422 INFO::Running selected normalization method: TSS
## 2023-06-12 11:36:15.122563 INFO::Bypass z-score application to metadata
## 2023-06-12 11:36:15.124053 INFO::Running selected transform method: LOG
## 2023-06-12 11:36:15.173854 INFO::Running selected analysis method: LM
## 2023-06-12 11:36:16.061689 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:16.718743 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2023-06-12 11:36:17.028233 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2023-06-12 11:36:17.327363 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:17.595133 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2023-06-12 11:36:17.880864 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:18.154347 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2023-06-12 11:36:18.412652 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2023-06-12 11:36:18.704018 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2023-06-12 11:36:18.967731 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2023-06-12 11:36:19.279011 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:19.550952 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:19.818645 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:20.11767 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2023-06-12 11:36:20.384241 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:20.656336 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2023-06-12 11:36:20.954046 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2023-06-12 11:36:21.270065 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:21.555992 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:21.830627 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:22.128611 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:22.403357 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2023-06-12 11:36:22.677801 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2023-06-12 11:36:22.987553 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2023-06-12 11:36:23.280931 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2023-06-12 11:36:23.560754 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:23.870256 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2023-06-12 11:36:24.169052 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2023-06-12 11:36:24.455497 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:24.746159 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2023-06-12 11:36:25.028725 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2023-06-12 11:36:25.308042 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:25.616766 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:25.893877 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
## 2023-06-12 11:36:26.121689 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
## 2023-06-12 11:36:26.429023 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:26.69386 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2023-06-12 11:36:26.986672 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2023-06-12 11:36:27.236745 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2023-06-12 11:36:27.509155 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:27.8242 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:28.105662 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:28.411572 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:28.689218 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2023-06-12 11:36:29.00547 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2023-06-12 11:36:29.298931 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:29.577401 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:29.894222 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2023-06-12 11:36:30.179327 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2023-06-12 11:36:30.488267 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:30.793699 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:31.087375 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:31.351146 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:31.62136 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:31.881745 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2023-06-12 11:36:32.166169 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2023-06-12 11:36:32.454712 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2023-06-12 11:36:32.758569 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:33.066793 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:33.360506 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:33.668221 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:34.012803 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2023-06-12 11:36:34.282606 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:34.564137 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:35.174134 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2023-06-12 11:36:35.464858 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2023-06-12 11:36:35.730414 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2023-06-12 11:36:36.001688 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:36.281555 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2023-06-12 11:36:36.5476 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2023-06-12 11:36:36.84245 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:37.137395 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2023-06-12 11:36:37.415128 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2023-06-12 11:36:37.739206 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:38.014748 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2023-06-12 11:36:38.302216 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:38.584674 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:39.184674 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2023-06-12 11:36:39.451491 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2023-06-12 11:36:39.709993 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2023-06-12 11:36:39.984943 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2023-06-12 11:36:40.326295 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2023-06-12 11:36:40.64166 INFO::Fitting model to feature number 82, Escherichia.coli
## 2023-06-12 11:36:40.953725 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2023-06-12 11:36:41.244947 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:41.521176 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2023-06-12 11:36:41.818354 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2023-06-12 11:36:42.114779 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2023-06-12 11:36:42.494764 INFO::Counting total values for each feature
## 2023-06-12 11:36:42.549944 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2023-06-12 11:36:42.77121 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2023-06-12 11:36:43.03791 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2023-06-12 11:36:43.350222 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2023-06-12 11:36:43.45636 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2023-06-12 11:36:43.515567 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2023-06-12 11:36:43.52776 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2023-06-12 11:36:43.536935 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
## 2023-06-12 11:36:43.541895 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2023-06-12 11:36:43.968942 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2023-06-12 11:36:43.979652 INFO::Plotting associations from most to least significant, grouped by metadata
## 2023-06-12 11:36:43.981325 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2023-06-12 11:36:43.984542 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2023-06-12 11:36:44.589854 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2023-06-12 11:36:45.102371 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2023-06-12 11:36:45.588919 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2023-06-12 11:36:46.089264 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2023-06-12 11:36:46.57358 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2023-06-12 11:36:47.042284 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2023-06-12 11:36:47.499014 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2023-06-12 11:36:47.936667 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2023-06-12 11:36:48.415501 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2023-06-12 11:36:48.904298 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2023-06-12 11:36:49.384962 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2023-06-12 11:36:49.864884 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2023-06-12 11:36:50.323336 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2023-06-12 11:36:50.76977 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2023-06-12 11:36:51.190913 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2023-06-12 11:36:51.668592 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2023-06-12 11:36:52.163593 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2023-06-12 11:36:52.639001 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2023-06-12 11:36:53.131511 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-06-12 11:36:53.592475 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2023-06-12 11:36:54.026526 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2023-06-12 11:36:54.470548 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2023-06-12 11:36:54.916537 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2023-06-12 11:36:55.41235 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2023-06-12 11:36:55.894759 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2023-06-12 11:36:56.334356 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2023-06-12 11:36:56.882748 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2023-06-12 11:36:57.343362 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2023-06-12 11:36:57.743921 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2023-06-12 11:36:58.120458 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2023-06-12 11:36:58.49493 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2023-06-12 11:36:58.895855 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2023-06-12 11:36:59.270504 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2023-06-12 11:36:59.692441 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2023-06-12 11:37:00.079045 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2023-06-12 11:37:00.4866 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2023-06-12 11:37:00.903139 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2023-06-12 11:37:01.289437 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2023-06-12 11:37:01.694467 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2023-06-12 11:37:02.063645 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2023-06-12 11:37:02.479117 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2023-06-12 11:37:02.844123 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2023-06-12 11:37:03.192917 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2023-06-12 11:37:03.644509 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2023-06-12 11:37:04.139097 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2023-06-12 11:37:04.597857 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2023-06-12 11:37:05.06781 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2023-06-12 11:37:05.468963 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2023-06-12 11:37:05.955711 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2023-06-12 11:37:06.395166 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2023-06-12 11:37:06.816747 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2023-06-12 11:37:07.313568 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2023-06-12 11:37:07.776681 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2023-06-12 11:37:08.218036 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2023-06-12 11:37:08.704162 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2023-06-12 11:37:09.201957 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2023-06-12 11:37:09.647239 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2023-06-12 11:37:10.142259 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2023-06-12 11:37:10.653485 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2023-06-12 11:37:11.102092 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2023-06-12 11:37:11.670631 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2023-06-12 11:37:12.139999 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2023-06-12 11:37:18.586779 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2023-06-12 11:37:18.590868 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2023-06-12 11:37:18.998037 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2023-06-12 11:37:19.452219 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2023-06-12 11:37:19.967891 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2023-06-12 11:37:20.488793 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2023-06-12 11:37:20.992178 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2023-06-12 11:37:21.53541 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2023-06-12 11:37:22.05591 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2023-06-12 11:37:22.531425 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2023-06-12 11:37:23.014271 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2023-06-12 11:37:23.494585 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2023-06-12 11:37:24.050933 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2023-06-12 11:37:24.584147 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-06-12 11:37:25.088568 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2023-06-12 11:37:25.636177 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2023-06-12 11:37:26.196357 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2023-06-12 11:37:26.653526 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2023-06-12 11:37:27.116465 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2023-06-12 11:37:27.60982 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2023-06-12 11:37:28.04631 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2023-06-12 11:37:28.508425 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2023-06-12 11:37:28.970658 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2023-06-12 11:37:29.431408 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2023-06-12 11:37:30.042582 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2023-06-12 11:37:30.551699 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2023-06-12 11:37:31.065712 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2023-06-12 11:37:31.617385 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2023-06-12 11:37:32.085427 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2023-06-12 11:37:32.620548 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2023-06-12 11:37:33.100062 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2023-06-12 11:37:33.595536 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2023-06-12 11:37:34.077214 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2023-06-12 11:37:34.57161 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2023-06-12 11:37:35.09616 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2023-06-12 11:37:35.620473 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2023-06-12 11:37:36.119052 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2023-06-12 11:37:36.610699 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2023-06-12 11:37:37.058039 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2023-06-12 11:37:37.576875 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2023-06-12 11:37:38.132322 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2023-06-12 11:37:38.638609 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2023-06-12 11:37:39.129947 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2023-06-12 11:37:39.620293 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2023-06-12 11:37:40.099003 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2023-06-12 11:37:46.715223 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2023-06-12 11:37:46.720473 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2023-06-12 11:37:47.173792 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2023-06-12 11:37:47.665454 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2023-06-12 11:37:48.317575 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2023-06-12 11:37:48.803566 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2023-06-12 11:37:49.367493 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-06-12 11:37:49.933371 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2023-06-12 11:37:50.446882 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2023-06-12 11:37:51.021183 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2023-06-12 11:37:51.514717 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2023-06-12 11:37:52.007846 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2023-06-12 11:37:52.498506 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2023-06-12 11:37:52.997118 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2023-06-12 11:37:53.545846 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2023-06-12 11:37:54.086118 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2023-06-12 11:37:54.602989 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2023-06-12 11:37:55.111951 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2023-06-12 11:37:55.578533 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2023-06-12 11:37:56.080156 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2023-06-12 11:37:56.634775 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2023-06-12 11:37:57.141049 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2023-06-12 11:37:57.68506 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2023-06-12 11:37:58.199747 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2023-06-12 11:37:58.64991 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2023-06-12 11:37:59.152103 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2023-06-12 11:37:59.699145 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2023-06-12 11:38:00.224718 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2023-06-12 11:38:00.739196 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2023-06-12 11:38:01.255952 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2023-06-12 11:38:07.770711 INFO::Plotting data for metadata number 4, antibiotics
## 2023-06-12 11:38:07.773639 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2023-06-12 11:38:08.265693 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2023-06-12 11:38:08.787591 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2023-06-12 11:38:09.285342 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2023-06-12 11:38:09.791599 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2023-06-12 11:38:10.219587 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2023-06-12 11:38:10.746381 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2023-06-12 11:38:11.235752 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2023-06-12 11:38:11.760416 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2023-06-12 11:38:12.280466 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2023-06-12 11:38:12.762581 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2023-06-12 11:38:13.246998 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2023-06-12 11:38:13.659193 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2023-06-12 11:38:14.211503 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2023-06-12 11:38:14.745886 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2023-06-12 11:38:15.234316 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-06-12 11:38:15.746701 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2023-06-12 11:38:16.175889 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2023-06-12 11:38:16.654702 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2023-06-12 11:38:17.171641 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2023-06-12 11:38:17.629383 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2023-06-12 11:38:18.220295 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2023-06-12 11:38:18.786265 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2023-06-12 11:38:19.258464 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2023-06-12 11:38:19.787086 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2023-06-12 11:38:20.29322 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2023-06-12 11:38:20.733315 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2023-06-12 11:38:21.227472 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2023-06-12 11:38:21.710426 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2023-06-12 11:38:22.211631 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2023-06-12 11:38:22.739081 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2023-06-12 11:38:23.703068 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2023-06-12 11:38:24.122157 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2023-06-12 11:38:24.576473 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2023-06-12 11:38:25.005605 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2023-06-12 11:38:25.461609 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2023-06-12 11:38:25.890952 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2023-06-12 11:38:26.32659 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2023-06-12 11:38:26.72025 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2023-06-12 11:38:27.133426 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2023-06-12 11:38:32.805471 INFO::Plotting data for metadata number 5, age
## 2023-06-12 11:38:32.811797 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()`).
## 2023-06-12 11:38:33.34658 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()`).
## 2023-06-12 11:38:33.953932 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()`).
## 2023-06-12 11:38:34.420488 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()`).
## 2023-06-12 11:38:34.923112 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()`).
## 2023-06-12 11:38:35.354845 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()`).
## 2023-06-12 11:38:35.806362 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()`).
## 2023-06-12 11:38:36.267411 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()`).
## 2023-06-12 11:38:36.749872 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()`).
## 2023-06-12 11:38:37.21706 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()`).
## 2023-06-12 11:38:37.681193 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()`).
## 2023-06-12 11:38:38.125277 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()`).
## 2023-06-12 11:38:38.568861 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()`).
## 2023-06-12 11:38:39.035452 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()`).
## 2023-06-12 11:38:39.498255 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()`).
## 2023-06-12 11:38:40.046785 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()`).
## 2023-06-12 11:38:40.556458 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()`).
## 2023-06-12 11:38:41.053233 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()`).
## 2023-06-12 11:38:41.479458 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()`).
## 2023-06-12 11:38:41.930074 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()`).
## 2023-06-12 11:38:42.418526 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()`).
## 2023-06-12 11:38:42.864193 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()`).
## 2023-06-12 11:38:49.232981 INFO::Plotting data for metadata number 6, diagnosis
## 2023-06-12 11:38:49.237256 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2023-06-12 11:38:49.665803 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2023-06-12 11:38:50.179792 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2023-06-12 11:38:50.650804 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2023-06-12 11:38:51.094556 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2023-06-12 11:38:51.604097 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2023-06-12 11:38:52.093038 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2023-06-12 11:38:52.566371 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2023-06-12 11:38:53.075357 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2023-06-12 11:38:53.580303 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2023-06-12 11:38:54.04441 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2023-06-12 11:38:54.543956 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2023-06-12 11:38:55.077067 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2023-06-12 11:38:55.681579 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2023-06-12 11:38:56.196662 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2023-06-12 11:38:56.721547 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2023-06-12 11:38:57.180212 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2023-06-12 11:38:57.70692 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2023-06-12 11:38:58.24436 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2023-06-12 11:38:58.751151 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2023-06-12 11:38:59.277476 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2023-06-12 11:38:59.813257 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2023-06-12 11:39:00.275172 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2023-06-12 11:39:00.767017 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2023-06-12 11:39:01.284731 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2023-06-12 11:39:01.778243 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2023-06-12 11:39:02.29746 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2023-06-12 11:39:02.824228 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2023-06-12 11:39:03.27003 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2023-06-12 11:39:03.757007 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2023-06-12 11:39:04.278147 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2023-06-12 11:39:04.758867 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2023-06-12 11:39:05.278642 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2023-06-12 11:39:05.783481 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2023-06-12 11:39:06.230217 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2023-06-12 11:39:06.721452 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2023-06-12 11:39:07.230835 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2023-06-12 11:39:07.680177 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2023-06-12 11:39:08.144466 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2023-06-12 11:39:08.655588 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2023-06-12 11:39:09.21987 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2023-06-12 11:39:09.811129 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2023-06-12 11:39:10.312292 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 4.3.0 RC (2023-04-13 r84266)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Monterey 12.6.1
## 
## 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_1.14.1
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.3        biglm_0.9-2.1       xfun_0.38          
##  [4] bslib_0.4.2         ggplot2_3.4.2       lattice_0.21-8     
##  [7] numDeriv_2016.8-1.1 vctrs_0.6.1         tools_4.3.0        
## [10] generics_0.1.3      parallel_4.3.0      getopt_1.20.3      
## [13] tibble_3.2.1        fansi_1.0.4         DEoptimR_1.0-12    
## [16] cluster_2.1.4       pkgconfig_2.0.3     logging_0.10-108   
## [19] pheatmap_1.0.12     Matrix_1.5-4        data.table_1.14.8  
## [22] RColorBrewer_1.1-3  lifecycle_1.0.3     farver_2.1.1       
## [25] compiler_4.3.0      munsell_0.5.0       lmerTest_3.1-3     
## [28] permute_0.9-7       htmltools_0.5.5     sass_0.4.5         
## [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_7.3-58.4       cachem_1.0.7        vegan_2.6-4        
## [40] boot_1.3-28.1       nlme_3.1-162        robustbase_0.95-1  
## [43] tidyselect_1.2.0    digest_0.6.31       mvtnorm_1.1-3      
## [46] dplyr_1.1.1         labeling_0.4.2      splines_4.3.0      
## [49] pcaPP_2.0-3         fastmap_1.1.1       grid_4.3.0         
## [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_2.21      lme4_1.1-32         pbapply_1.7-0      
## [61] evaluate_0.20       knitr_1.42          mgcv_1.8-42        
## [64] rlang_1.1.0         Rcpp_1.0.10         glue_1.6.2         
## [67] optparse_1.7.3      DBI_1.1.3           minqa_1.2.5        
## [70] jsonlite_1.8.4      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.