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)
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.
MaAsLin2 is an R package that can be run on the command line or as an R function.
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.
$ tar xzvf maaslin2.tar.gz
$ 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')"
$ R CMD INSTALL maaslin2
Install Bioconductor and then install Maaslin2
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Maaslin2")
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.
MaAsLin2 requires two input files.
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.
MaAsLin2 generates two types of output files: data and visualization.
all_results.tsv
N
column is the total number of data points.N.not.zero
column is the total of non-zero data points.p.adjust
with the correction method.significant_results.tsv
models.rds
residuals.rds
fitted.rds
ranef.rds
maaslin2.log
heatmap.pdf
[a-z/0-9]+.pdf
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.
$ 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
HMP2_taxonomy.tsv
is the path to your data (or features) fileHMP2_metadata.tsv
is the path to your metadata filedemo_output
is the path to the folder to write the outputlibrary(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"
## 2025-04-22 19:12:07.160244 INFO::Writing function arguments to log file
## 2025-04-22 19:12:07.193945 INFO::Verifying options selected are valid
## 2025-04-22 19:12:07.23796 INFO::Determining format of input files
## 2025-04-22 19:12:07.248428 INFO::Input format is data samples as rows and metadata samples as rows
## 2025-04-22 19:12:07.255835 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2025-04-22 19:12:07.257629 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2025-04-22 19:12:07.260613 INFO::Filter data based on min abundance and min prevalence
## 2025-04-22 19:12:07.261853 INFO::Total samples in data: 1595
## 2025-04-22 19:12:07.262716 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2025-04-22 19:12:07.26754 INFO::Total filtered features: 0
## 2025-04-22 19:12:07.268739 INFO::Filtered feature names from abundance and prevalence filtering:
## 2025-04-22 19:12:07.277153 INFO::Total filtered features with variance filtering: 0
## 2025-04-22 19:12:07.2784 INFO::Filtered feature names from variance filtering:
## 2025-04-22 19:12:07.279299 INFO::Running selected normalization method: TSS
## 2025-04-22 19:12:08.339148 INFO::Bypass z-score application to metadata
## 2025-04-22 19:12:08.340413 INFO::Running selected transform method: LOG
## 2025-04-22 19:12:08.356886 INFO::Running selected analysis method: LM
## 2025-04-22 19:12:08.709319 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:09.081842 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2025-04-22 19:12:09.226827 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2025-04-22 19:12:09.449481 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:09.822782 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2025-04-22 19:12:09.977857 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:10.142948 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2025-04-22 19:12:10.308973 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2025-04-22 19:12:10.456965 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2025-04-22 19:12:10.608909 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2025-04-22 19:12:10.779141 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
## boundary (singular) fit: see help('isSingular')
## Feature Bacteroides.finegoldii : simpleWarning: Model failed to converge with 1 negative eigenvalue: -7.9e+01
## 2025-04-22 19:12:10.898336 WARNING::Fitting problem for feature 11 a warning was issued
## boundary (singular) fit: see help('isSingular')
## Warning: Model failed to converge with 1 negative eigenvalue: -7.9e+01
## 2025-04-22 19:12:11.03324 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:11.167433 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:11.306492 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2025-04-22 19:12:11.459499 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:11.608567 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2025-04-22 19:12:11.738022 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2025-04-22 19:12:11.863748 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:12.001019 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:12.132938 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:12.291252 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:12.428949 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2025-04-22 19:12:12.577866 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2025-04-22 19:12:12.707589 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2025-04-22 19:12:12.837015 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2025-04-22 19:12:12.969296 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:13.124277 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2025-04-22 19:12:13.274675 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2025-04-22 19:12:13.403085 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:13.547979 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2025-04-22 19:12:13.7057 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2025-04-22 19:12:13.859831 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:14.003612 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:14.140283 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:14.284585 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:14.414862 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2025-04-22 19:12:14.538568 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2025-04-22 19:12:14.67562 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2025-04-22 19:12:14.841699 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:15.001641 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## Feature Clostridium.citroniae : simpleWarning: Model failed to converge with 1 negative eigenvalue: -3.4e+01
## 2025-04-22 19:12:15.108126 WARNING::Fitting problem for feature 40 a warning was issued
## boundary (singular) fit: see help('isSingular')
## Warning: Model failed to converge with 1 negative eigenvalue: -3.4e+01
## 2025-04-22 19:12:15.255908 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:15.380508 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:15.516123 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2025-04-22 19:12:15.687713 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2025-04-22 19:12:15.814988 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:15.953705 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:16.098483 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2025-04-22 19:12:16.238529 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2025-04-22 19:12:16.369235 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:16.535905 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:16.686969 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:16.825302 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:16.94948 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:17.08156 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2025-04-22 19:12:17.206568 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2025-04-22 19:12:17.354901 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2025-04-22 19:12:17.503391 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:17.649048 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:18.029042 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:18.15564 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:18.297176 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2025-04-22 19:12:18.433061 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:18.563071 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:18.682274 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2025-04-22 19:12:18.835801 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2025-04-22 19:12:18.990396 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2025-04-22 19:12:19.120045 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:19.246858 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2025-04-22 19:12:19.381639 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2025-04-22 19:12:19.500211 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:19.616797 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2025-04-22 19:12:19.737993 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2025-04-22 19:12:19.863454 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:20.001569 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2025-04-22 19:12:20.143879 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:20.285106 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:20.419933 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2025-04-22 19:12:20.557658 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2025-04-22 19:12:20.70758 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2025-04-22 19:12:20.846497 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2025-04-22 19:12:20.988331 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2025-04-22 19:12:21.102954 INFO::Fitting model to feature number 82, Escherichia.coli
## 2025-04-22 19:12:21.224368 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2025-04-22 19:12:21.348838 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:21.470923 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2025-04-22 19:12:21.608283 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2025-04-22 19:12:21.76331 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2025-04-22 19:12:21.923281 INFO::Counting total values for each feature
## 2025-04-22 19:12:21.948554 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2025-04-22 19:12:22.052839 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2025-04-22 19:12:22.180873 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2025-04-22 19:12:22.362003 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2025-04-22 19:12:22.413241 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2025-04-22 19:12:22.443484 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2025-04-22 19:12:22.685956 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2025-04-22 19:12:22.693908 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
## 2025-04-22 19:12:22.697461 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2025-04-22 19:12:22.832604 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2025-04-22 19:12:22.839343 INFO::Plotting associations from most to least significant, grouped by metadata
## 2025-04-22 19:12:22.84063 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2025-04-22 19:12:22.842726 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2025-04-22 19:12:23.173475 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2025-04-22 19:12:23.48444 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2025-04-22 19:12:23.737747 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2025-04-22 19:12:24.01412 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2025-04-22 19:12:24.276166 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2025-04-22 19:12:24.532271 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2025-04-22 19:12:24.811098 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2025-04-22 19:12:25.081888 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2025-04-22 19:12:25.337714 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2025-04-22 19:12:25.623653 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2025-04-22 19:12:25.883241 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2025-04-22 19:12:26.167095 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2025-04-22 19:12:26.439773 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2025-04-22 19:12:26.720068 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2025-04-22 19:12:27.006663 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2025-04-22 19:12:27.290272 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2025-04-22 19:12:27.598161 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2025-04-22 19:12:27.875916 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2025-04-22 19:12:28.15521 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-22 19:12:28.432205 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2025-04-22 19:12:28.713305 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2025-04-22 19:12:28.982356 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2025-04-22 19:12:29.49228 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2025-04-22 19:12:29.709997 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2025-04-22 19:12:29.98588 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2025-04-22 19:12:30.216413 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2025-04-22 19:12:30.4776 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2025-04-22 19:12:30.733228 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2025-04-22 19:12:30.967213 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2025-04-22 19:12:31.21631 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2025-04-22 19:12:31.45843 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2025-04-22 19:12:31.70234 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2025-04-22 19:12:31.9473 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2025-04-22 19:12:32.173497 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2025-04-22 19:12:32.40656 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2025-04-22 19:12:32.655536 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2025-04-22 19:12:32.921259 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2025-04-22 19:12:33.16346 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2025-04-22 19:12:33.417856 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2025-04-22 19:12:33.701997 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2025-04-22 19:12:33.95396 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2025-04-22 19:12:34.221993 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2025-04-22 19:12:34.490602 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2025-04-22 19:12:34.806208 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2025-04-22 19:12:35.109825 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2025-04-22 19:12:35.418622 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2025-04-22 19:12:35.718991 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2025-04-22 19:12:35.972518 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2025-04-22 19:12:36.268503 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2025-04-22 19:12:36.5451 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2025-04-22 19:12:36.827397 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2025-04-22 19:12:37.093475 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2025-04-22 19:12:37.357649 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2025-04-22 19:12:37.600136 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2025-04-22 19:12:37.887347 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2025-04-22 19:12:38.167486 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2025-04-22 19:12:38.446865 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2025-04-22 19:12:38.734297 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2025-04-22 19:12:39.004428 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2025-04-22 19:12:39.280809 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2025-04-22 19:12:39.530952 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2025-04-22 19:12:39.866404 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2025-04-22 19:12:42.721569 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2025-04-22 19:12:42.723603 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2025-04-22 19:12:42.99588 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2025-04-22 19:12:43.278396 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2025-04-22 19:12:43.570858 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2025-04-22 19:12:43.843706 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2025-04-22 19:12:44.146797 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2025-04-22 19:12:44.417811 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2025-04-22 19:12:44.715456 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2025-04-22 19:12:44.96608 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2025-04-22 19:12:45.258166 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2025-04-22 19:12:45.536595 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2025-04-22 19:12:45.797666 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2025-04-22 19:12:46.060733 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-22 19:12:46.35264 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2025-04-22 19:12:46.667145 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2025-04-22 19:12:46.949373 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2025-04-22 19:12:47.224017 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2025-04-22 19:12:47.486485 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2025-04-22 19:12:47.794696 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2025-04-22 19:12:48.06001 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2025-04-22 19:12:48.345034 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2025-04-22 19:12:48.643007 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2025-04-22 19:12:48.944887 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2025-04-22 19:12:49.272651 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2025-04-22 19:12:49.56743 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2025-04-22 19:12:49.876877 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2025-04-22 19:12:50.173285 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2025-04-22 19:12:50.436606 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2025-04-22 19:12:50.723258 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2025-04-22 19:12:51.054835 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2025-04-22 19:12:51.333306 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2025-04-22 19:12:51.629221 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2025-04-22 19:12:51.935218 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2025-04-22 19:12:52.220186 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2025-04-22 19:12:52.51391 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2025-04-22 19:12:52.787453 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2025-04-22 19:12:53.093694 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2025-04-22 19:12:53.378026 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2025-04-22 19:12:53.709099 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2025-04-22 19:12:53.991171 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2025-04-22 19:12:54.287119 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2025-04-22 19:12:54.583089 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2025-04-22 19:12:54.907501 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2025-04-22 19:12:55.23809 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2025-04-22 19:12:58.629183 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2025-04-22 19:12:58.631616 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2025-04-22 19:12:58.891933 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2025-04-22 19:12:59.230174 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2025-04-22 19:12:59.533093 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2025-04-22 19:12:59.829503 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2025-04-22 19:13:00.108122 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-22 19:13:00.431979 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2025-04-22 19:13:00.74062 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2025-04-22 19:13:01.036937 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2025-04-22 19:13:01.327549 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2025-04-22 19:13:01.60122 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2025-04-22 19:13:01.886349 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2025-04-22 19:13:02.183609 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2025-04-22 19:13:02.503912 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2025-04-22 19:13:02.851585 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2025-04-22 19:13:03.159274 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2025-04-22 19:13:03.459448 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2025-04-22 19:13:03.745345 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2025-04-22 19:13:04.074057 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2025-04-22 19:13:04.339978 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2025-04-22 19:13:04.638405 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2025-04-22 19:13:04.915857 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2025-04-22 19:13:05.211034 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2025-04-22 19:13:05.47917 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2025-04-22 19:13:05.776018 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2025-04-22 19:13:06.073384 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2025-04-22 19:13:06.37252 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2025-04-22 19:13:06.68048 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2025-04-22 19:13:06.959461 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2025-04-22 19:13:09.875916 INFO::Plotting data for metadata number 4, antibiotics
## 2025-04-22 19:13:09.877984 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2025-04-22 19:13:10.084483 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2025-04-22 19:13:10.358168 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2025-04-22 19:13:10.600824 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2025-04-22 19:13:10.843504 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2025-04-22 19:13:11.104914 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2025-04-22 19:13:11.358597 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2025-04-22 19:13:11.613875 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2025-04-22 19:13:11.895656 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2025-04-22 19:13:12.138723 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2025-04-22 19:13:12.400366 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2025-04-22 19:13:12.67229 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2025-04-22 19:13:12.93831 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2025-04-22 19:13:13.239318 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2025-04-22 19:13:13.455072 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2025-04-22 19:13:13.754704 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-22 19:13:14.013241 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2025-04-22 19:13:14.297379 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2025-04-22 19:13:14.515257 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2025-04-22 19:13:14.74476 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2025-04-22 19:13:14.983125 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2025-04-22 19:13:15.240189 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2025-04-22 19:13:15.469704 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2025-04-22 19:13:15.738163 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2025-04-22 19:13:16.009459 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2025-04-22 19:13:16.300484 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2025-04-22 19:13:16.548662 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2025-04-22 19:13:16.838718 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2025-04-22 19:13:17.071486 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2025-04-22 19:13:17.36161 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2025-04-22 19:13:17.59799 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2025-04-22 19:13:17.861873 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2025-04-22 19:13:18.089833 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2025-04-22 19:13:18.360596 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2025-04-22 19:13:18.579419 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2025-04-22 19:13:18.843129 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2025-04-22 19:13:19.091808 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2025-04-22 19:13:19.372735 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2025-04-22 19:13:19.67737 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2025-04-22 19:13:19.947219 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2025-04-22 19:13:22.754708 INFO::Plotting data for metadata number 5, age
## 2025-04-22 19:13:22.757148 INFO::Creating scatter plot for continuous data, age vs Haemophilus.parainfluenzae
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:23.076478 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.pseudocatenulatum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:23.451694 INFO::Creating scatter plot for continuous data, age vs Faecalibacterium.prausnitzii
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:23.732332 INFO::Creating scatter plot for continuous data, age vs Clostridium.clostridioforme
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:24.034996 INFO::Creating scatter plot for continuous data, age vs Veillonella.parvula
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:24.418806 INFO::Creating scatter plot for continuous data, age vs Subdoligranulum.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:24.74094 INFO::Creating scatter plot for continuous data, age vs Clostridium.symbiosum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:25.032149 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.gnavus
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:25.345837 INFO::Creating scatter plot for continuous data, age vs Dialister.invisus
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:25.621897 INFO::Creating scatter plot for continuous data, age vs Veillonella.dispar
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:25.927761 INFO::Creating scatter plot for continuous data, age vs Veillonella.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:26.231023 INFO::Creating scatter plot for continuous data, age vs Bacteroides.thetaiotaomicron
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:26.493 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.bromii
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:26.789091 INFO::Creating scatter plot for continuous data, age vs Bacteroides.intestinalis
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:27.114799 INFO::Creating scatter plot for continuous data, age vs Eubacterium.siraeum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:27.397315 INFO::Creating scatter plot for continuous data, age vs Prevotella.copri
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:27.678707 INFO::Creating scatter plot for continuous data, age vs Alistipes.unclassified
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:27.985015 INFO::Creating scatter plot for continuous data, age vs Bacteroidales.bacterium.ph8
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:28.276111 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.longum
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:28.572876 INFO::Creating scatter plot for continuous data, age vs Akkermansia.muciniphila
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:28.860628 INFO::Creating scatter plot for continuous data, age vs Collinsella.aerofaciens
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:29.140696 INFO::Creating scatter plot for continuous data, age vs Parabacteroides.distasonis
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## `geom_smooth()` using formula = 'y ~ x'
## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).
## 2025-04-22 19:13:32.242129 INFO::Plotting data for metadata number 6, diagnosis
## 2025-04-22 19:13:32.245108 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2025-04-22 19:13:32.612178 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2025-04-22 19:13:33.009647 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2025-04-22 19:13:33.379352 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2025-04-22 19:13:33.786383 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2025-04-22 19:13:34.179095 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2025-04-22 19:13:34.455418 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2025-04-22 19:13:34.995891 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2025-04-22 19:13:35.24839 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2025-04-22 19:13:35.511034 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2025-04-22 19:13:35.770165 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2025-04-22 19:13:36.040061 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2025-04-22 19:13:36.317012 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2025-04-22 19:13:36.594612 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2025-04-22 19:13:36.848208 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2025-04-22 19:13:37.095777 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2025-04-22 19:13:37.320249 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2025-04-22 19:13:37.588314 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2025-04-22 19:13:37.860324 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2025-04-22 19:13:38.094725 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2025-04-22 19:13:38.3559 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2025-04-22 19:13:38.619725 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2025-04-22 19:13:38.880009 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2025-04-22 19:13:39.151452 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2025-04-22 19:13:39.405277 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2025-04-22 19:13:39.679457 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2025-04-22 19:13:39.942733 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2025-04-22 19:13:40.218173 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2025-04-22 19:13:40.476228 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2025-04-22 19:13:40.728684 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2025-04-22 19:13:40.991988 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2025-04-22 19:13:41.256659 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2025-04-22 19:13:41.523774 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2025-04-22 19:13:41.803015 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2025-04-22 19:13:42.050188 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2025-04-22 19:13:42.334104 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2025-04-22 19:13:42.589997 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2025-04-22 19:13:42.82111 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2025-04-22 19:13:43.076378 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2025-04-22 19:13:43.339885 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2025-04-22 19:13:43.618115 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2025-04-22 19:13:43.87403 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2025-04-22 19:13:44.170024 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.siraeum
Session info from running the demo in R can be displayed with the following command.
sessionInfo()
## R version 4.5.0 Patched (2025-04-21 r88169)
## Platform: x86_64-apple-darwin20
## Running under: macOS Monterey 12.7.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
##
## 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_1.23.0
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.6 biglm_0.9-3 xfun_0.52
## [4] bslib_0.9.0 ggplot2_3.5.2 lattice_0.22-7
## [7] numDeriv_2016.8-1.1 vctrs_0.6.5 tools_4.5.0
## [10] Rdpack_2.6.4 generics_0.1.3 parallel_4.5.0
## [13] getopt_1.20.4 tibble_3.2.1 DEoptimR_1.1-3-1
## [16] cluster_2.1.8.1 pkgconfig_2.0.3 logging_0.10-108
## [19] pheatmap_1.0.12 Matrix_1.7-3 data.table_1.17.0
## [22] RColorBrewer_1.1-3 lifecycle_1.0.4 farver_2.1.2
## [25] compiler_4.5.0 munsell_0.5.1 lmerTest_3.1-3
## [28] permute_0.9-7 htmltools_0.5.8.1 sass_0.4.10
## [31] hash_2.2.6.3 yaml_2.3.10 pillar_1.10.2
## [34] nloptr_2.2.1 crayon_1.5.3 jquerylib_0.1.4
## [37] MASS_7.3-65 cachem_1.1.0 vegan_2.6-10
## [40] reformulas_0.4.0 boot_1.3-31 nlme_3.1-168
## [43] robustbase_0.99-4-1 tidyselect_1.2.1 digest_0.6.37
## [46] mvtnorm_1.3-3 dplyr_1.1.4 labeling_0.4.3
## [49] splines_4.5.0 pcaPP_2.0-5 fastmap_1.2.0
## [52] grid_4.5.0 colorspace_2.1-1 cli_3.6.4
## [55] magrittr_2.0.3 withr_3.0.2 scales_1.3.0
## [58] rmarkdown_2.29 lme4_1.1-37 pbapply_1.7-2
## [61] evaluate_1.0.3 knitr_1.50 rbibutils_2.3
## [64] mgcv_1.9-3 rlang_1.1.6 Rcpp_1.0.14
## [67] glue_1.8.0 optparse_1.7.5 DBI_1.2.3
## [70] minqa_1.2.8 jsonlite_2.0.0 R6_2.6.1
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 ]
Maaslin2.R: command not found
. How do I fix this?
Error in library(Maaslin2): there is no package called 'Maaslin2'
. How do I fix this?