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"
## 2023-06-13 19:06:06.496713 INFO::Writing function arguments to log file
## 2023-06-13 19:06:06.568601 INFO::Verifying options selected are valid
## 2023-06-13 19:06:06.649637 INFO::Determining format of input files
## 2023-06-13 19:06:06.652286 INFO::Input format is data samples as rows and metadata samples as rows
## 2023-06-13 19:06:06.666395 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2023-06-13 19:06:06.668801 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2023-06-13 19:06:06.674879 INFO::Filter data based on min abundance and min prevalence
## 2023-06-13 19:06:06.678764 INFO::Total samples in data: 1595
## 2023-06-13 19:06:06.680704 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2023-06-13 19:06:06.694149 INFO::Total filtered features: 0
## 2023-06-13 19:06:06.738618 INFO::Filtered feature names from abundance and prevalence filtering:
## 2023-06-13 19:06:06.758083 INFO::Total filtered features with variance filtering: 0
## 2023-06-13 19:06:06.761457 INFO::Filtered feature names from variance filtering:
## 2023-06-13 19:06:06.763222 INFO::Running selected normalization method: TSS
## 2023-06-13 19:06:09.630144 INFO::Bypass z-score application to metadata
## 2023-06-13 19:06:09.632919 INFO::Running selected transform method: LOG
## 2023-06-13 19:06:09.700064 INFO::Running selected analysis method: LM
## 2023-06-13 19:06:10.867984 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:11.890316 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2023-06-13 19:06:12.337784 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2023-06-13 19:06:12.747892 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:13.119471 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2023-06-13 19:06:13.530747 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:13.908533 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2023-06-13 19:06:14.272291 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2023-06-13 19:06:14.66574 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2023-06-13 19:06:15.084153 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2023-06-13 19:06:15.530521 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:15.906805 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:16.279562 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:16.660618 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2023-06-13 19:06:17.007922 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:17.366033 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2023-06-13 19:06:17.756899 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2023-06-13 19:06:18.120114 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:18.475582 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:18.828995 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:19.202001 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:19.558843 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2023-06-13 19:06:19.925475 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2023-06-13 19:06:20.316612 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2023-06-13 19:06:20.725962 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2023-06-13 19:06:21.079202 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:21.439809 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2023-06-13 19:06:21.801775 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2023-06-13 19:06:22.159752 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:22.525221 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2023-06-13 19:06:22.901897 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2023-06-13 19:06:23.283759 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:23.672572 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:24.031974 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:24.40655 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:24.77367 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2023-06-13 19:06:25.131894 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2023-06-13 19:06:25.486512 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2023-06-13 19:06:25.843077 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:26.216012 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:26.585279 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:26.943129 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:27.322746 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2023-06-13 19:06:27.698822 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2023-06-13 19:06:28.055139 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:28.422686 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:28.823372 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2023-06-13 19:06:29.186311 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2023-06-13 19:06:29.56112 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:29.963337 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:30.352935 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:30.760765 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:31.142084 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:31.52379 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2023-06-13 19:06:31.893824 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2023-06-13 19:06:32.288462 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2023-06-13 19:06:32.664199 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:33.047813 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:33.431162 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:33.788343 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:34.162963 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2023-06-13 19:06:34.556638 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:34.909597 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:35.281992 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2023-06-13 19:06:35.68561 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2023-06-13 19:06:36.062668 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2023-06-13 19:06:36.452261 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:36.811958 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2023-06-13 19:06:37.189609 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2023-06-13 19:06:37.574528 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:37.93812 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2023-06-13 19:06:38.300239 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2023-06-13 19:06:38.681696 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:39.055497 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2023-06-13 19:06:39.441983 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:39.808288 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:40.159969 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2023-06-13 19:06:40.521614 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2023-06-13 19:06:40.897899 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2023-06-13 19:06:41.260179 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2023-06-13 19:06:41.591062 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2023-06-13 19:06:42.114186 INFO::Fitting model to feature number 82, Escherichia.coli
## 2023-06-13 19:06:42.681702 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2023-06-13 19:06:43.107526 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:43.651313 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2023-06-13 19:06:44.249917 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2023-06-13 19:06:44.696146 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2023-06-13 19:06:45.975871 INFO::Counting total values for each feature
## 2023-06-13 19:06:46.066197 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2023-06-13 19:06:46.544471 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2023-06-13 19:06:47.073558 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2023-06-13 19:06:47.799585 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2023-06-13 19:06:47.91885 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2023-06-13 19:06:47.987606 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2023-06-13 19:06:48.000786 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2023-06-13 19:06:48.062951 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
## 2023-06-13 19:06:48.071792 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2023-06-13 19:06:49.022674 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2023-06-13 19:06:49.036584 INFO::Plotting associations from most to least significant, grouped by metadata
## 2023-06-13 19:06:49.039568 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2023-06-13 19:06:49.046597 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2023-06-13 19:06:50.353255 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2023-06-13 19:06:51.119547 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2023-06-13 19:06:52.198653 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2023-06-13 19:06:53.01228 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2023-06-13 19:06:53.927203 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2023-06-13 19:06:54.86112 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2023-06-13 19:06:55.62982 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2023-06-13 19:06:56.718408 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2023-06-13 19:06:57.382591 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2023-06-13 19:06:58.001531 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2023-06-13 19:06:58.5983 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2023-06-13 19:06:59.208543 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2023-06-13 19:06:59.82437 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2023-06-13 19:07:00.452625 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2023-06-13 19:07:01.082715 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2023-06-13 19:07:01.67992 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2023-06-13 19:07:02.313787 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2023-06-13 19:07:02.955875 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2023-06-13 19:07:03.567322 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-06-13 19:07:04.141324 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2023-06-13 19:07:04.713776 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2023-06-13 19:07:05.63927 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2023-06-13 19:07:06.203869 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2023-06-13 19:07:06.764278 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2023-06-13 19:07:07.365255 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2023-06-13 19:07:07.937343 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2023-06-13 19:07:08.549857 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2023-06-13 19:07:09.103497 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2023-06-13 19:07:09.674541 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2023-06-13 19:07:10.283571 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2023-06-13 19:07:10.842568 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2023-06-13 19:07:11.433828 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2023-06-13 19:07:11.9864 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2023-06-13 19:07:12.560524 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2023-06-13 19:07:13.159161 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2023-06-13 19:07:13.710777 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2023-06-13 19:07:14.320174 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2023-06-13 19:07:14.923385 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2023-06-13 19:07:15.502257 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2023-06-13 19:07:16.110182 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2023-06-13 19:07:16.677322 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2023-06-13 19:07:17.243896 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2023-06-13 19:07:17.799061 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2023-06-13 19:07:18.38099 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2023-06-13 19:07:18.961715 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2023-06-13 19:07:19.5932 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2023-06-13 19:07:20.195521 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2023-06-13 19:07:20.875185 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2023-06-13 19:07:21.51877 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2023-06-13 19:07:22.11779 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2023-06-13 19:07:22.755581 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2023-06-13 19:07:23.35627 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2023-06-13 19:07:23.956366 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2023-06-13 19:07:24.572309 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2023-06-13 19:07:25.187666 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2023-06-13 19:07:25.809028 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2023-06-13 19:07:26.433344 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2023-06-13 19:07:27.027316 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2023-06-13 19:07:27.649339 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2023-06-13 19:07:28.223068 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2023-06-13 19:07:28.831985 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2023-06-13 19:07:29.42743 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2023-06-13 19:07:37.106833 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2023-06-13 19:07:37.11082 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2023-06-13 19:07:37.672559 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2023-06-13 19:07:38.258868 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2023-06-13 19:07:38.922045 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2023-06-13 19:07:39.526502 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2023-06-13 19:07:40.120825 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2023-06-13 19:07:40.744335 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2023-06-13 19:07:41.352378 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2023-06-13 19:07:41.951218 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2023-06-13 19:07:42.578728 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2023-06-13 19:07:43.178443 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2023-06-13 19:07:43.764522 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2023-06-13 19:07:44.351658 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-06-13 19:07:45.054759 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2023-06-13 19:07:45.668063 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2023-06-13 19:07:46.278685 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2023-06-13 19:07:46.874606 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2023-06-13 19:07:47.532778 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2023-06-13 19:07:48.233855 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2023-06-13 19:07:48.821359 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2023-06-13 19:07:49.438982 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2023-06-13 19:07:50.081672 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2023-06-13 19:07:50.66296 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2023-06-13 19:07:51.316935 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2023-06-13 19:07:51.940354 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2023-06-13 19:07:52.548669 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2023-06-13 19:07:53.146012 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2023-06-13 19:07:53.764561 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2023-06-13 19:07:54.374547 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2023-06-13 19:07:54.942081 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2023-06-13 19:07:55.525322 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2023-06-13 19:07:56.096301 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2023-06-13 19:07:56.702904 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2023-06-13 19:07:57.263864 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2023-06-13 19:07:57.849598 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2023-06-13 19:07:58.441717 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2023-06-13 19:07:59.059896 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2023-06-13 19:07:59.657335 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2023-06-13 19:08:00.272839 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2023-06-13 19:08:00.91811 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2023-06-13 19:08:01.510064 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2023-06-13 19:08:02.139381 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2023-06-13 19:08:02.776667 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2023-06-13 19:08:03.370708 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2023-06-13 19:08:11.198387 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2023-06-13 19:08:11.204331 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2023-06-13 19:08:11.76719 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2023-06-13 19:08:12.422131 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2023-06-13 19:08:13.073889 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2023-06-13 19:08:13.71426 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2023-06-13 19:08:14.331513 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-06-13 19:08:14.945127 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2023-06-13 19:08:15.583027 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2023-06-13 19:08:16.222831 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2023-06-13 19:08:16.808554 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2023-06-13 19:08:17.409061 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2023-06-13 19:08:17.989101 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2023-06-13 19:08:18.636132 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2023-06-13 19:08:19.262525 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2023-06-13 19:08:19.873586 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2023-06-13 19:08:20.520578 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2023-06-13 19:08:21.12352 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2023-06-13 19:08:21.713055 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2023-06-13 19:08:22.339968 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2023-06-13 19:08:22.955287 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2023-06-13 19:08:23.538785 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2023-06-13 19:08:24.149797 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2023-06-13 19:08:24.785469 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2023-06-13 19:08:25.414739 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2023-06-13 19:08:26.03561 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2023-06-13 19:08:26.664567 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2023-06-13 19:08:27.247937 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2023-06-13 19:08:27.831525 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2023-06-13 19:08:28.453113 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2023-06-13 19:08:36.051042 INFO::Plotting data for metadata number 4, antibiotics
## 2023-06-13 19:08:36.057252 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2023-06-13 19:08:36.581375 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2023-06-13 19:08:37.178824 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2023-06-13 19:08:37.77097 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2023-06-13 19:08:38.354649 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2023-06-13 19:08:38.954828 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2023-06-13 19:08:39.500938 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2023-06-13 19:08:40.108258 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2023-06-13 19:08:40.66191 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2023-06-13 19:08:41.26107 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2023-06-13 19:08:41.868034 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2023-06-13 19:08:42.418608 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2023-06-13 19:08:43.018518 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2023-06-13 19:08:43.59779 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2023-06-13 19:08:44.184433 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2023-06-13 19:08:44.760194 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2023-06-13 19:08:45.319761 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2023-06-13 19:08:45.882678 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2023-06-13 19:08:46.446392 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2023-06-13 19:08:47.011491 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2023-06-13 19:08:47.607734 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2023-06-13 19:08:48.176478 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2023-06-13 19:08:48.745259 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2023-06-13 19:08:49.333673 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2023-06-13 19:08:49.876286 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2023-06-13 19:08:50.484269 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2023-06-13 19:08:51.069752 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2023-06-13 19:08:51.621086 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2023-06-13 19:08:52.251114 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2023-06-13 19:08:52.845984 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2023-06-13 19:08:53.385146 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2023-06-13 19:08:53.952996 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2023-06-13 19:08:54.53121 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2023-06-13 19:08:55.179141 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2023-06-13 19:08:55.730312 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2023-06-13 19:08:56.328063 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2023-06-13 19:08:56.9611 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2023-06-13 19:08:57.575576 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2023-06-13 19:08:58.149469 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2023-06-13 19:08:58.714545 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2023-06-13 19:09:06.45186 INFO::Plotting data for metadata number 5, age
## 2023-06-13 19:09:06.456636 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()`).
## 2023-06-13 19:09:07.20865 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()`).
## 2023-06-13 19:09:08.101596 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()`).
## 2023-06-13 19:09:08.78345 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()`).
## 2023-06-13 19:09:09.473502 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()`).
## 2023-06-13 19:09:10.160996 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()`).
## 2023-06-13 19:09:10.826733 INFO::Creating scatter plot for continuous data, age vs Clostridium.symbiosum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-06-13 19:09:11.560477 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()`).
## 2023-06-13 19:09:12.254324 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()`).
## 2023-06-13 19:09:12.938958 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()`).
## 2023-06-13 19:09:14.039324 INFO::Creating scatter plot for continuous data, age vs Veillonella.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-06-13 19:09:14.658235 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()`).
## 2023-06-13 19:09:15.288796 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()`).
## 2023-06-13 19:09:15.932077 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()`).
## 2023-06-13 19:09:16.557471 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()`).
## 2023-06-13 19:09:17.144413 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()`).
## 2023-06-13 19:09:17.777165 INFO::Creating scatter plot for continuous data, age vs Alistipes.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-06-13 19:09:18.375698 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()`).
## 2023-06-13 19:09:18.962156 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()`).
## 2023-06-13 19:09:19.554517 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()`).
## 2023-06-13 19:09:20.18218 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()`).
## 2023-06-13 19:09:20.791599 INFO::Creating scatter plot for continuous data, age vs Parabacteroides.distasonis
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values (`geom_point()`).
## 2023-06-13 19:09:28.590658 INFO::Plotting data for metadata number 6, diagnosis
## 2023-06-13 19:09:28.594468 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2023-06-13 19:09:29.127141 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2023-06-13 19:09:29.742191 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2023-06-13 19:09:30.325692 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2023-06-13 19:09:30.898434 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2023-06-13 19:09:31.467258 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2023-06-13 19:09:32.065793 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2023-06-13 19:09:32.644474 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2023-06-13 19:09:33.267053 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2023-06-13 19:09:33.92276 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2023-06-13 19:09:34.533989 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2023-06-13 19:09:35.168104 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2023-06-13 19:09:35.879489 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2023-06-13 19:09:36.58063 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2023-06-13 19:09:37.300238 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2023-06-13 19:09:37.985954 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2023-06-13 19:09:38.67753 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2023-06-13 19:09:39.368989 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2023-06-13 19:09:40.123261 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2023-06-13 19:09:40.845195 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2023-06-13 19:09:41.537046 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2023-06-13 19:09:42.26248 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2023-06-13 19:09:42.957873 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2023-06-13 19:09:43.666432 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2023-06-13 19:09:44.389668 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2023-06-13 19:09:45.086376 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2023-06-13 19:09:45.761399 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2023-06-13 19:09:46.476092 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2023-06-13 19:09:47.187294 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2023-06-13 19:09:47.858642 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2023-06-13 19:09:48.555172 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2023-06-13 19:09:49.21147 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2023-06-13 19:09:49.89717 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2023-06-13 19:09:50.602632 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2023-06-13 19:09:51.288061 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2023-06-13 19:09:51.974007 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2023-06-13 19:09:52.651543 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2023-06-13 19:09:53.317526 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2023-06-13 19:09:54.026118 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2023-06-13 19:09:54.682266 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2023-06-13 19:09:55.357265 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2023-06-13 19:09:56.135659 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2023-06-13 19:09:56.841224 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 r84257)
## Platform: x86_64-apple-darwin20 (64-bit)
## Running under: macOS Monterey 12.6.4
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/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_0.39          
##  [4] bslib_0.5.0         ggplot2_3.4.2       lattice_0.21-8     
##  [7] numDeriv_2016.8-1.1 vctrs_0.6.2         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_1.0-14    
## [16] cluster_2.1.4       pkgconfig_2.0.3     logging_0.10-108   
## [19] pheatmap_1.0.12     Matrix_1.5-4.1      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_0.4.6         
## [31] hash_2.2.6.2        yaml_2.3.7          pillar_1.9.0       
## [34] nloptr_2.0.3        crayon_1.5.2        jquerylib_0.1.4    
## [37] MASS_7.3-60         cachem_1.0.8        vegan_2.6-4        
## [40] boot_1.3-28.1       nlme_3.1-162        robustbase_0.95-1  
## [43] tidyselect_1.2.0    digest_0.6.31       mvtnorm_1.2-2      
## [46] dplyr_1.1.2         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_2.22      lme4_1.1-33         pbapply_1.7-0      
## [61] evaluate_0.21       knitr_1.43          mgcv_1.8-42        
## [64] rlang_1.1.1         Rcpp_1.0.10         glue_1.6.2         
## [67] optparse_1.7.3      DBI_1.1.3           minqa_1.2.5        
## [70] jsonlite_1.8.5      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.