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"
## 2025-04-15 20:50:01.354369 INFO::Writing function arguments to log file
## 2025-04-15 20:50:01.391361 INFO::Verifying options selected are valid
## 2025-04-15 20:50:01.425949 INFO::Determining format of input files
## 2025-04-15 20:50:01.428109 INFO::Input format is data samples as rows and metadata samples as rows
## 2025-04-15 20:50:01.435428 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2025-04-15 20:50:01.437484 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2025-04-15 20:50:01.440549 INFO::Filter data based on min abundance and min prevalence
## 2025-04-15 20:50:01.445826 INFO::Total samples in data: 1595
## 2025-04-15 20:50:01.4474 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2025-04-15 20:50:01.452748 INFO::Total filtered features: 0
## 2025-04-15 20:50:01.454567 INFO::Filtered feature names from abundance and prevalence filtering:
## 2025-04-15 20:50:01.463722 INFO::Total filtered features with variance filtering: 0
## 2025-04-15 20:50:01.465735 INFO::Filtered feature names from variance filtering:
## 2025-04-15 20:50:01.467289 INFO::Running selected normalization method: TSS
## 2025-04-15 20:50:02.511573 INFO::Bypass z-score application to metadata
## 2025-04-15 20:50:02.513482 INFO::Running selected transform method: LOG
## 2025-04-15 20:50:02.536312 INFO::Running selected analysis method: LM
## 2025-04-15 20:50:02.85653 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:03.273601 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2025-04-15 20:50:03.674281 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2025-04-15 20:50:03.831643 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:03.992046 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2025-04-15 20:50:04.188081 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:04.338756 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2025-04-15 20:50:04.471064 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2025-04-15 20:50:04.610601 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2025-04-15 20:50:04.740225 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2025-04-15 20:50:04.891648 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
## 2025-04-15 20:50:05.000782 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
## 2025-04-15 20:50:05.154582 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:05.313685 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:05.482311 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2025-04-15 20:50:05.646056 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:05.80346 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2025-04-15 20:50:06.032942 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2025-04-15 20:50:06.248621 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:06.461821 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:06.689759 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:06.848975 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:07.009495 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2025-04-15 20:50:07.153025 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2025-04-15 20:50:07.362602 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2025-04-15 20:50:07.513398 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2025-04-15 20:50:07.703719 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:07.852607 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2025-04-15 20:50:08.040857 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2025-04-15 20:50:08.194548 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:08.320307 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2025-04-15 20:50:08.44952 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2025-04-15 20:50:08.599858 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:08.737617 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:08.872233 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:09.000435 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:09.141465 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2025-04-15 20:50:09.342957 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2025-04-15 20:50:09.552315 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2025-04-15 20:50:09.751268 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:09.895816 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
## 2025-04-15 20:50:10.006794 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
## 2025-04-15 20:50:10.161487 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:10.297247 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:10.472417 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2025-04-15 20:50:10.708611 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2025-04-15 20:50:10.85447 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:11.013753 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:11.177098 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2025-04-15 20:50:11.318193 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2025-04-15 20:50:11.45793 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:11.62382 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:11.757882 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:11.90258 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:12.053318 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:12.272605 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2025-04-15 20:50:12.480113 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2025-04-15 20:50:12.695855 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2025-04-15 20:50:12.918831 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:13.062805 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:13.296641 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:13.436095 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:13.576561 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2025-04-15 20:50:13.737664 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:13.870715 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:14.009128 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2025-04-15 20:50:14.176472 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2025-04-15 20:50:14.305525 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2025-04-15 20:50:14.434923 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:14.569625 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2025-04-15 20:50:14.696541 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2025-04-15 20:50:14.833665 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:14.973572 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2025-04-15 20:50:15.145721 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2025-04-15 20:50:15.362381 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:15.543153 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2025-04-15 20:50:15.712001 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:15.928192 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:16.10294 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2025-04-15 20:50:16.299372 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2025-04-15 20:50:16.464268 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2025-04-15 20:50:16.601759 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2025-04-15 20:50:16.734765 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2025-04-15 20:50:16.869342 INFO::Fitting model to feature number 82, Escherichia.coli
## 2025-04-15 20:50:17.015392 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2025-04-15 20:50:17.144993 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:17.286916 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2025-04-15 20:50:17.415339 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2025-04-15 20:50:17.565896 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2025-04-15 20:50:17.746884 INFO::Counting total values for each feature
## 2025-04-15 20:50:17.782743 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2025-04-15 20:50:18.097276 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2025-04-15 20:50:18.450185 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2025-04-15 20:50:18.925842 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2025-04-15 20:50:18.974426 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2025-04-15 20:50:19.011257 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2025-04-15 20:50:19.020137 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2025-04-15 20:50:19.046868 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
## 2025-04-15 20:50:19.059255 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2025-04-15 20:50:19.637186 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2025-04-15 20:50:19.645045 INFO::Plotting associations from most to least significant, grouped by metadata
## 2025-04-15 20:50:19.646943 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2025-04-15 20:50:19.649527 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2025-04-15 20:50:20.011481 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2025-04-15 20:50:20.596175 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2025-04-15 20:50:20.872433 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2025-04-15 20:50:21.157155 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2025-04-15 20:50:21.410967 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2025-04-15 20:50:22.059698 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2025-04-15 20:50:22.347243 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2025-04-15 20:50:22.62151 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2025-04-15 20:50:22.881749 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2025-04-15 20:50:23.178891 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2025-04-15 20:50:23.635929 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2025-04-15 20:50:24.038329 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2025-04-15 20:50:24.3993 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2025-04-15 20:50:24.692373 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2025-04-15 20:50:24.940795 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2025-04-15 20:50:25.358326 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2025-04-15 20:50:25.70157 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2025-04-15 20:50:25.967326 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2025-04-15 20:50:26.27095 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-15 20:50:26.688829 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2025-04-15 20:50:27.079756 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2025-04-15 20:50:27.433362 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2025-04-15 20:50:27.733292 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2025-04-15 20:50:28.050668 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2025-04-15 20:50:28.309744 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2025-04-15 20:50:28.589296 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2025-04-15 20:50:28.86331 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2025-04-15 20:50:29.197193 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2025-04-15 20:50:29.58672 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2025-04-15 20:50:29.865883 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2025-04-15 20:50:30.188091 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2025-04-15 20:50:30.491637 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2025-04-15 20:50:30.830609 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2025-04-15 20:50:31.194521 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2025-04-15 20:50:31.589229 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2025-04-15 20:50:31.921723 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2025-04-15 20:50:32.246912 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2025-04-15 20:50:32.55313 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2025-04-15 20:50:32.836077 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2025-04-15 20:50:33.234451 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2025-04-15 20:50:33.649394 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2025-04-15 20:50:34.025375 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2025-04-15 20:50:34.375704 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2025-04-15 20:50:34.622065 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2025-04-15 20:50:34.884178 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2025-04-15 20:50:35.12935 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2025-04-15 20:50:35.402567 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2025-04-15 20:50:35.65776 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2025-04-15 20:50:35.935121 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2025-04-15 20:50:36.188353 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2025-04-15 20:50:36.475203 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2025-04-15 20:50:36.742924 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2025-04-15 20:50:37.005683 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2025-04-15 20:50:37.361551 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2025-04-15 20:50:37.644463 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2025-04-15 20:50:37.907494 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2025-04-15 20:50:38.149522 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2025-04-15 20:50:38.405099 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2025-04-15 20:50:38.659819 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2025-04-15 20:50:38.989028 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2025-04-15 20:50:39.360127 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2025-04-15 20:50:39.78687 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2025-04-15 20:50:43.437668 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2025-04-15 20:50:43.440414 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2025-04-15 20:50:43.657527 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2025-04-15 20:50:43.92817 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2025-04-15 20:50:44.814445 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2025-04-15 20:50:45.181043 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2025-04-15 20:50:45.433698 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2025-04-15 20:50:45.711952 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2025-04-15 20:50:45.986567 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2025-04-15 20:50:46.295358 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2025-04-15 20:50:46.605706 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2025-04-15 20:50:46.982036 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2025-04-15 20:50:47.267132 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2025-04-15 20:50:47.694285 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-15 20:50:48.102063 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2025-04-15 20:50:48.367317 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2025-04-15 20:50:48.647579 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2025-04-15 20:50:48.949479 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2025-04-15 20:50:49.261461 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2025-04-15 20:50:49.524943 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2025-04-15 20:50:49.853888 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2025-04-15 20:50:50.12658 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2025-04-15 20:50:50.401248 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2025-04-15 20:50:50.665836 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2025-04-15 20:50:50.954053 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2025-04-15 20:50:51.224556 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2025-04-15 20:50:51.504535 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2025-04-15 20:50:51.783492 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2025-04-15 20:50:52.041806 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2025-04-15 20:50:52.396285 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2025-04-15 20:50:52.665466 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2025-04-15 20:50:53.052513 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2025-04-15 20:50:53.352319 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2025-04-15 20:50:53.657005 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2025-04-15 20:50:53.978445 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2025-04-15 20:50:54.272558 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2025-04-15 20:50:54.528619 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2025-04-15 20:50:54.823666 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2025-04-15 20:50:55.092468 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2025-04-15 20:50:55.650659 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2025-04-15 20:50:55.916954 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2025-04-15 20:50:56.216505 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2025-04-15 20:50:56.554132 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2025-04-15 20:50:57.019617 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2025-04-15 20:50:57.281766 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2025-04-15 20:51:01.116345 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2025-04-15 20:51:01.119359 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2025-04-15 20:51:01.350214 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2025-04-15 20:51:01.630191 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2025-04-15 20:51:01.889078 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2025-04-15 20:51:02.15145 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2025-04-15 20:51:02.438875 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-15 20:51:02.713454 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2025-04-15 20:51:02.962098 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2025-04-15 20:51:03.247725 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2025-04-15 20:51:03.506 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2025-04-15 20:51:03.788123 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2025-04-15 20:51:04.061131 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2025-04-15 20:51:04.332161 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2025-04-15 20:51:04.617593 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2025-04-15 20:51:04.903005 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2025-04-15 20:51:05.228531 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2025-04-15 20:51:05.477765 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2025-04-15 20:51:05.758849 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2025-04-15 20:51:06.026078 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2025-04-15 20:51:06.312826 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2025-04-15 20:51:06.568794 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2025-04-15 20:51:06.969815 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2025-04-15 20:51:07.370706 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2025-04-15 20:51:07.689298 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2025-04-15 20:51:07.949046 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2025-04-15 20:51:08.242404 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2025-04-15 20:51:08.517645 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2025-04-15 20:51:08.790027 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2025-04-15 20:51:09.078325 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2025-04-15 20:51:12.89997 INFO::Plotting data for metadata number 4, antibiotics
## 2025-04-15 20:51:12.904272 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2025-04-15 20:51:13.471355 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2025-04-15 20:51:13.835368 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2025-04-15 20:51:14.102271 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2025-04-15 20:51:14.393284 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2025-04-15 20:51:14.642777 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2025-04-15 20:51:14.923762 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2025-04-15 20:51:15.178118 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2025-04-15 20:51:15.459329 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2025-04-15 20:51:15.765437 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2025-04-15 20:51:16.044877 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2025-04-15 20:51:16.285532 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2025-04-15 20:51:16.554618 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2025-04-15 20:51:16.816933 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2025-04-15 20:51:17.070091 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2025-04-15 20:51:17.341999 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2025-04-15 20:51:17.588983 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2025-04-15 20:51:17.913364 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2025-04-15 20:51:18.176929 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2025-04-15 20:51:18.454413 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2025-04-15 20:51:18.723306 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2025-04-15 20:51:19.057748 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2025-04-15 20:51:19.348683 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2025-04-15 20:51:19.621369 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2025-04-15 20:51:19.884572 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2025-04-15 20:51:20.185185 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2025-04-15 20:51:20.482011 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2025-04-15 20:51:20.750816 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2025-04-15 20:51:21.048409 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2025-04-15 20:51:21.41295 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2025-04-15 20:51:21.702643 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2025-04-15 20:51:21.969963 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2025-04-15 20:51:22.239443 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2025-04-15 20:51:22.559393 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2025-04-15 20:51:22.914479 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2025-04-15 20:51:23.196146 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2025-04-15 20:51:23.458093 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2025-04-15 20:51:23.730043 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2025-04-15 20:51:23.991076 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2025-04-15 20:51:24.277854 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2025-04-15 20:51:28.080233 INFO::Plotting data for metadata number 5, age
## 2025-04-15 20:51:28.083041 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()`).
## 2025-04-15 20:51:28.372391 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()`).
## 2025-04-15 20:51:28.770034 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()`).
## 2025-04-15 20:51:29.0675 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()`).
## 2025-04-15 20:51:29.865608 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()`).
## 2025-04-15 20:51:30.20554 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()`).
## 2025-04-15 20:51:30.514366 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()`).
## 2025-04-15 20:51:31.252486 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()`).
## 2025-04-15 20:51:31.556181 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()`).
## 2025-04-15 20:51:31.941976 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()`).
## 2025-04-15 20:51:32.272957 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()`).
## 2025-04-15 20:51:32.526257 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()`).
## 2025-04-15 20:51:32.76252 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()`).
## 2025-04-15 20:51:33.010912 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()`).
## 2025-04-15 20:51:33.242813 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()`).
## 2025-04-15 20:51:33.47746 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()`).
## 2025-04-15 20:51:33.716887 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()`).
## 2025-04-15 20:51:33.973373 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()`).
## 2025-04-15 20:51:34.273723 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()`).
## 2025-04-15 20:51:34.576367 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()`).
## 2025-04-15 20:51:34.830249 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()`).
## 2025-04-15 20:51:35.124145 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()`).
## 2025-04-15 20:51:39.250218 INFO::Plotting data for metadata number 6, diagnosis
## 2025-04-15 20:51:39.253055 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2025-04-15 20:51:39.484779 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2025-04-15 20:51:39.735921 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2025-04-15 20:51:40.03413 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2025-04-15 20:51:40.42477 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2025-04-15 20:51:40.697377 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2025-04-15 20:51:40.943045 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2025-04-15 20:51:41.207279 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2025-04-15 20:51:41.526309 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2025-04-15 20:51:41.779068 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2025-04-15 20:51:42.050161 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2025-04-15 20:51:42.346925 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2025-04-15 20:51:42.672556 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2025-04-15 20:51:43.014333 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2025-04-15 20:51:43.497663 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2025-04-15 20:51:43.913293 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2025-04-15 20:51:44.197387 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2025-04-15 20:51:44.449854 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2025-04-15 20:51:44.736424 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2025-04-15 20:51:45.019468 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2025-04-15 20:51:45.295255 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2025-04-15 20:51:45.551393 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2025-04-15 20:51:45.835503 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2025-04-15 20:51:46.11368 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2025-04-15 20:51:46.461912 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2025-04-15 20:51:46.855296 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2025-04-15 20:51:47.116635 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2025-04-15 20:51:47.402056 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2025-04-15 20:51:47.657258 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2025-04-15 20:51:47.932967 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2025-04-15 20:51:48.219339 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2025-04-15 20:51:48.649038 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2025-04-15 20:51:49.052722 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2025-04-15 20:51:49.413443 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2025-04-15 20:51:49.750319 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2025-04-15 20:51:50.188526 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2025-04-15 20:51:50.532254 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2025-04-15 20:51:50.797676 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2025-04-15 20:51:51.074519 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2025-04-15 20:51:51.514191 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2025-04-15 20:51:51.86327 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2025-04-15 20:51:52.119849 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2025-04-15 20:51:52.483121 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 RC (2025-04-03 r88103 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows Server 2022 x64 (build 20348)
##
## Matrix products: default
## LAPACK version 3.12.1
##
## locale:
## [1] LC_COLLATE=C
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## 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?