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 maaslin2Install 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"
## 2024-12-18 17:43:44.885695 INFO::Writing function arguments to log file
## 2024-12-18 17:43:44.90908 INFO::Verifying options selected are valid
## 2024-12-18 17:43:44.944934 INFO::Determining format of input files
## 2024-12-18 17:43:44.94613 INFO::Input format is data samples as rows and metadata samples as rows
## 2024-12-18 17:43:44.950496 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2024-12-18 17:43:44.951496 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2024-12-18 17:43:44.953555 INFO::Filter data based on min abundance and min prevalence
## 2024-12-18 17:43:44.95421 INFO::Total samples in data: 1595
## 2024-12-18 17:43:44.954823 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2024-12-18 17:43:44.959492 INFO::Total filtered features: 0
## 2024-12-18 17:43:44.960285 INFO::Filtered feature names from abundance and prevalence filtering:
## 2024-12-18 17:43:44.96867 INFO::Total filtered features with variance filtering: 0
## 2024-12-18 17:43:44.969483 INFO::Filtered feature names from variance filtering:
## 2024-12-18 17:43:44.970108 INFO::Running selected normalization method: TSS
## 2024-12-18 17:43:45.959147 INFO::Bypass z-score application to metadata
## 2024-12-18 17:43:45.960135 INFO::Running selected transform method: LOG
## 2024-12-18 17:43:45.976411 INFO::Running selected analysis method: LM
## 2024-12-18 17:43:46.256048 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:46.546887 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2024-12-18 17:43:46.970124 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2024-12-18 17:43:47.100835 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:47.240525 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2024-12-18 17:43:47.404824 INFO::Fitting model to feature number 6, Bacteroides.caccae## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:47.550875 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2024-12-18 17:43:47.682817 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2024-12-18 17:43:47.829319 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2024-12-18 17:43:47.971063 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2024-12-18 17:43:48.115911 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## 2024-12-18 17:43:48.227219 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## 2024-12-18 17:43:48.3619 INFO::Fitting model to feature number 12, Bacteroides.fragilis## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:48.498588 INFO::Fitting model to feature number 13, Bacteroides.intestinalis## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:48.633858 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2024-12-18 17:43:48.766583 INFO::Fitting model to feature number 15, Bacteroides.ovatus## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:48.89284 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2024-12-18 17:43:49.032439 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2024-12-18 17:43:49.168576 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:49.300757 INFO::Fitting model to feature number 19, Bacteroides.uniformis## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:49.446909 INFO::Fitting model to feature number 20, Bacteroides.vulgatus## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:49.582522 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:49.724546 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2024-12-18 17:43:49.865454 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2024-12-18 17:43:50.014977 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2024-12-18 17:43:50.161533 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2024-12-18 17:43:50.317055 INFO::Fitting model to feature number 26, Parabacteroides.distasonis## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:50.459964 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2024-12-18 17:43:50.599615 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2024-12-18 17:43:50.742407 INFO::Fitting model to feature number 29, Parabacteroides.unclassified## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:50.877713 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2024-12-18 17:43:51.013627 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2024-12-18 17:43:51.150296 INFO::Fitting model to feature number 32, Prevotella.copri## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:51.284261 INFO::Fitting model to feature number 33, Alistipes.finegoldii## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:51.41564 INFO::Fitting model to feature number 34, Alistipes.onderdonkii## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:51.556079 INFO::Fitting model to feature number 35, Alistipes.putredinis## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:51.688818 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2024-12-18 17:43:51.83136 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2024-12-18 17:43:51.958375 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2024-12-18 17:43:52.095111 INFO::Fitting model to feature number 39, Clostridium.bolteae## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:52.239018 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## 2024-12-18 17:43:52.353124 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## 2024-12-18 17:43:52.735866 INFO::Fitting model to feature number 41, Clostridium.clostridioforme## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:52.862007 INFO::Fitting model to feature number 42, Clostridium.hathewayi## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:52.993855 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2024-12-18 17:43:53.142546 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2024-12-18 17:43:53.280129 INFO::Fitting model to feature number 45, Clostridium.symbiosum## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:53.409396 INFO::Fitting model to feature number 46, Flavonifractor.plautii## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:53.545186 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2024-12-18 17:43:53.682183 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2024-12-18 17:43:53.819753 INFO::Fitting model to feature number 49, Eubacterium.rectale## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:53.958784 INFO::Fitting model to feature number 50, Eubacterium.siraeum## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:54.095345 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:54.227448 INFO::Fitting model to feature number 52, Eubacterium.ventriosum## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:54.353504 INFO::Fitting model to feature number 53, Ruminococcus.gnavus## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:54.492833 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2024-12-18 17:43:54.619666 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2024-12-18 17:43:54.74913 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2024-12-18 17:43:54.901141 INFO::Fitting model to feature number 57, Dorea.longicatena## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:55.044758 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:55.190613 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:55.339132 INFO::Fitting model to feature number 60, Roseburia.hominis## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:55.473497 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2024-12-18 17:43:55.600919 INFO::Fitting model to feature number 62, Roseburia.inulinivorans## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:55.7391 INFO::Fitting model to feature number 63, Roseburia.unclassified## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:55.870523 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2024-12-18 17:43:56.240819 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2024-12-18 17:43:56.371557 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2024-12-18 17:43:56.502417 INFO::Fitting model to feature number 67, Ruminococcus.bromii## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:56.626632 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2024-12-18 17:43:56.952933 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2024-12-18 17:43:57.09007 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:57.227216 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2024-12-18 17:43:57.366185 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2024-12-18 17:43:57.504313 INFO::Fitting model to feature number 73, Dialister.invisus## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:57.642116 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2024-12-18 17:43:57.800253 INFO::Fitting model to feature number 75, Veillonella.dispar## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:57.937942 INFO::Fitting model to feature number 76, Veillonella.parvula## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:58.07109 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2024-12-18 17:43:58.209702 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2024-12-18 17:43:58.348172 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2024-12-18 17:43:58.479846 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2024-12-18 17:43:58.620736 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2024-12-18 17:43:58.760949 INFO::Fitting model to feature number 82, Escherichia.coli
## 2024-12-18 17:43:58.897326 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2024-12-18 17:43:59.032118 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:59.169543 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae## boundary (singular) fit: see help('isSingular')## 2024-12-18 17:43:59.300796 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2024-12-18 17:43:59.437925 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2024-12-18 17:43:59.615306 INFO::Counting total values for each feature
## 2024-12-18 17:43:59.644842 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2024-12-18 17:43:59.736193 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2024-12-18 17:43:59.830466 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2024-12-18 17:44:00.005429 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2024-12-18 17:44:00.060727 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2024-12-18 17:44:00.092226 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2024-12-18 17:44:00.09713 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2024-12-18 17:44:00.101734 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): demo_output/significant_results.tsv
## 2024-12-18 17:44:00.103914 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2024-12-18 17:44:00.312788 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2024-12-18 17:44:00.318358 INFO::Plotting associations from most to least significant, grouped by metadata
## 2024-12-18 17:44:00.319267 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2024-12-18 17:44:00.32075 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii## 2024-12-18 17:44:00.634382 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified## 2024-12-18 17:44:00.912844 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis## 2024-12-18 17:44:01.15351 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale## 2024-12-18 17:44:01.401449 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus## 2024-12-18 17:44:01.634911 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus## 2024-12-18 17:44:01.878565 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum## 2024-12-18 17:44:02.119725 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified## 2024-12-18 17:44:02.364545 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans## 2024-12-18 17:44:02.607146 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis## 2024-12-18 17:44:02.84943 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron## 2024-12-18 17:44:03.103632 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis## 2024-12-18 17:44:03.377782 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis## 2024-12-18 17:44:03.628365 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei## 2024-12-18 17:44:03.883528 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii## 2024-12-18 17:44:04.129349 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens## 2024-12-18 17:44:04.374727 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum## 2024-12-18 17:44:04.617218 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena## 2024-12-18 17:44:04.86531 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae## 2024-12-18 17:44:05.103042 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-12-18 17:44:05.353071 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli## 2024-12-18 17:44:05.590377 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae## 2024-12-18 17:44:05.830971 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified## 2024-12-18 17:44:06.058632 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii## 2024-12-18 17:44:06.302123 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens## 2024-12-18 17:44:06.542897 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris## 2024-12-18 17:44:06.805319 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes## 2024-12-18 17:44:07.06118 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis## 2024-12-18 17:44:07.295321 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii## 2024-12-18 17:44:07.533509 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii## 2024-12-18 17:44:07.764743 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis## 2024-12-18 17:44:08.30065 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara## 2024-12-18 17:44:08.530457 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum## 2024-12-18 17:44:08.758506 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae## 2024-12-18 17:44:08.989124 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified## 2024-12-18 17:44:09.224494 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens## 2024-12-18 17:44:09.456804 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus## 2024-12-18 17:44:09.698253 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme## 2024-12-18 17:44:09.93072 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii## 2024-12-18 17:44:10.167812 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii## 2024-12-18 17:44:10.395076 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum## 2024-12-18 17:44:10.632764 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris## 2024-12-18 17:44:10.862231 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47## 2024-12-18 17:44:11.102611 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus## 2024-12-18 17:44:11.337152 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii## 2024-12-18 17:44:11.576092 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis## 2024-12-18 17:44:11.803907 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified## 2024-12-18 17:44:12.044266 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques## 2024-12-18 17:44:12.265963 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified## 2024-12-18 17:44:12.51379 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus## 2024-12-18 17:44:12.743383 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis## 2024-12-18 17:44:12.981412 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified## 2024-12-18 17:44:13.212376 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified## 2024-12-18 17:44:13.449852 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis## 2024-12-18 17:44:13.67565 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis## 2024-12-18 17:44:13.918699 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31## 2024-12-18 17:44:14.14559 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae## 2024-12-18 17:44:14.377342 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8## 2024-12-18 17:44:14.601589 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae## 2024-12-18 17:44:14.834658 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii## 2024-12-18 17:44:15.067032 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii## 2024-12-18 17:44:15.3049 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum## 2024-12-18 17:44:15.529373 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA## 2024-12-18 17:44:18.544249 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2024-12-18 17:44:18.546067 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified## 2024-12-18 17:44:18.749043 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii## 2024-12-18 17:44:18.995672 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae## 2024-12-18 17:44:19.236821 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified## 2024-12-18 17:44:19.475482 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis## 2024-12-18 17:44:19.711662 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum## 2024-12-18 17:44:20.001877 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus## 2024-12-18 17:44:20.240496 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis## 2024-12-18 17:44:20.527228 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii## 2024-12-18 17:44:20.768482 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale## 2024-12-18 17:44:21.010932 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis## 2024-12-18 17:44:21.249246 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis## 2024-12-18 17:44:21.495111 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-12-18 17:44:21.729686 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii## 2024-12-18 17:44:21.97509 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens## 2024-12-18 17:44:22.21088 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris## 2024-12-18 17:44:22.460022 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii## 2024-12-18 17:44:22.702789 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis## 2024-12-18 17:44:22.95829 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum## 2024-12-18 17:44:23.188929 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus## 2024-12-18 17:44:23.43542 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii## 2024-12-18 17:44:23.676982 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii## 2024-12-18 17:44:23.923028 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae## 2024-12-18 17:44:24.160965 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus## 2024-12-18 17:44:24.408358 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum## 2024-12-18 17:44:24.642809 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae## 2024-12-18 17:44:24.905075 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae## 2024-12-18 17:44:25.166847 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum## 2024-12-18 17:44:25.407992 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis## 2024-12-18 17:44:25.650758 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii## 2024-12-18 17:44:25.885291 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques## 2024-12-18 17:44:26.118991 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8## 2024-12-18 17:44:26.360068 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum## 2024-12-18 17:44:26.596771 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum## 2024-12-18 17:44:26.835897 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis## 2024-12-18 17:44:27.072265 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens## 2024-12-18 17:44:27.302013 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi## 2024-12-18 17:44:27.547159 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified## 2024-12-18 17:44:27.779563 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens## 2024-12-18 17:44:28.025464 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus## 2024-12-18 17:44:28.263901 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae## 2024-12-18 17:44:28.515716 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus## 2024-12-18 17:44:28.764107 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris## 2024-12-18 17:44:28.999003 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47## 2024-12-18 17:44:32.061802 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2024-12-18 17:44:32.063708 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii## 2024-12-18 17:44:32.292885 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale## 2024-12-18 17:44:32.541844 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31## 2024-12-18 17:44:32.798391 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis## 2024-12-18 17:44:33.029685 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified## 2024-12-18 17:44:33.287011 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-12-18 17:44:33.53281 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques## 2024-12-18 17:44:33.794701 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum## 2024-12-18 17:44:34.06312 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus## 2024-12-18 17:44:34.324316 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli## 2024-12-18 17:44:34.558605 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum## 2024-12-18 17:44:34.809919 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified## 2024-12-18 17:44:35.053581 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis## 2024-12-18 17:44:35.308653 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens## 2024-12-18 17:44:35.558671 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae## 2024-12-18 17:44:35.820105 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii## 2024-12-18 17:44:36.054997 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus## 2024-12-18 17:44:36.307261 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified## 2024-12-18 17:44:36.563749 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis## 2024-12-18 17:44:36.826888 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii## 2024-12-18 17:44:37.079786 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans## 2024-12-18 17:44:37.324703 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii## 2024-12-18 17:44:37.581441 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified## 2024-12-18 17:44:37.823743 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii## 2024-12-18 17:44:38.075628 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis## 2024-12-18 17:44:38.317878 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri## 2024-12-18 17:44:38.575667 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei## 2024-12-18 17:44:38.811118 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis## 2024-12-18 17:44:39.071864 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii## 2024-12-18 17:44:42.23853 INFO::Plotting data for metadata number 4, antibiotics
## 2024-12-18 17:44:42.240475 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans## 2024-12-18 17:44:42.448921 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis## 2024-12-18 17:44:42.676455 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale## 2024-12-18 17:44:42.90361 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus## 2024-12-18 17:44:43.148944 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis## 2024-12-18 17:44:43.37389 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena## 2024-12-18 17:44:43.613055 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus## 2024-12-18 17:44:43.84489 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii## 2024-12-18 17:44:44.07976 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum## 2024-12-18 17:44:44.302104 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae## 2024-12-18 17:44:44.54302 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis## 2024-12-18 17:44:44.763484 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii## 2024-12-18 17:44:44.998555 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii## 2024-12-18 17:44:45.229672 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified## 2024-12-18 17:44:45.46588 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum## 2024-12-18 17:44:45.688639 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-12-18 17:44:45.922643 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii## 2024-12-18 17:44:46.148501 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31## 2024-12-18 17:44:46.380846 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis## 2024-12-18 17:44:46.601443 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii## 2024-12-18 17:44:46.838885 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis## 2024-12-18 17:44:47.07006 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens## 2024-12-18 17:44:47.304973 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens## 2024-12-18 17:44:47.53371 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron## 2024-12-18 17:44:47.768636 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii## 2024-12-18 17:44:47.998007 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae## 2024-12-18 17:44:48.231228 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum## 2024-12-18 17:44:48.463106 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques## 2024-12-18 17:44:48.709661 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum## 2024-12-18 17:44:48.940914 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis## 2024-12-18 17:44:49.174815 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified## 2024-12-18 17:44:49.403372 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar## 2024-12-18 17:44:49.648234 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica## 2024-12-18 17:44:49.878743 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8## 2024-12-18 17:44:50.118256 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile## 2024-12-18 17:44:50.343499 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47## 2024-12-18 17:44:50.578756 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA## 2024-12-18 17:44:50.809721 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila## 2024-12-18 17:44:51.07832 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae## 2024-12-18 17:44:51.32259 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus## 2024-12-18 17:44:54.296998 INFO::Plotting data for metadata number 5, age
## 2024-12-18 17:44:54.29892 INFO::Creating scatter plot for continuous data, age vs Haemophilus.parainfluenzae## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:54.576905 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.pseudocatenulatum## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:54.89583 INFO::Creating scatter plot for continuous data, age vs Faecalibacterium.prausnitzii## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:55.127352 INFO::Creating scatter plot for continuous data, age vs Clostridium.clostridioforme## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:55.388318 INFO::Creating scatter plot for continuous data, age vs Veillonella.parvula## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:55.617366 INFO::Creating scatter plot for continuous data, age vs Subdoligranulum.unclassified## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:55.867267 INFO::Creating scatter plot for continuous data, age vs Clostridium.symbiosum## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:56.11213 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.gnavus## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:56.363832 INFO::Creating scatter plot for continuous data, age vs Dialister.invisus## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:56.615184 INFO::Creating scatter plot for continuous data, age vs Veillonella.dispar## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:56.844777 INFO::Creating scatter plot for continuous data, age vs Veillonella.unclassified## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:57.087986 INFO::Creating scatter plot for continuous data, age vs Bacteroides.thetaiotaomicron## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:57.338668 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.bromii## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:57.581576 INFO::Creating scatter plot for continuous data, age vs Bacteroides.intestinalis## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:57.82707 INFO::Creating scatter plot for continuous data, age vs Eubacterium.siraeum## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:58.05465 INFO::Creating scatter plot for continuous data, age vs Prevotella.copri## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:58.318238 INFO::Creating scatter plot for continuous data, age vs Alistipes.unclassified## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:58.561921 INFO::Creating scatter plot for continuous data, age vs Bacteroidales.bacterium.ph8## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:58.784767 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.longum## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:59.063861 INFO::Creating scatter plot for continuous data, age vs Akkermansia.muciniphila## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:59.317843 INFO::Creating scatter plot for continuous data, age vs Collinsella.aerofaciens## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:44:59.549631 INFO::Creating scatter plot for continuous data, age vs Parabacteroides.distasonis## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values or values outside the scale range
## (`geom_point()`).## 2024-12-18 17:45:02.800318 INFO::Plotting data for metadata number 6, diagnosis
## 2024-12-18 17:45:02.802105 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis## 2024-12-18 17:45:03.013493 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila## 2024-12-18 17:45:03.243391 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae## 2024-12-18 17:45:03.468576 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis## 2024-12-18 17:45:03.706536 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified## 2024-12-18 17:45:03.933403 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme## 2024-12-18 17:45:04.163411 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii## 2024-12-18 17:45:04.390755 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii## 2024-12-18 17:45:04.630923 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum## 2024-12-18 17:45:04.862291 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum## 2024-12-18 17:45:05.099127 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans## 2024-12-18 17:45:05.331119 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii## 2024-12-18 17:45:05.568962 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii## 2024-12-18 17:45:05.809425 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii## 2024-12-18 17:45:06.038056 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii## 2024-12-18 17:45:06.285875 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified## 2024-12-18 17:45:06.515423 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum## 2024-12-18 17:45:06.760056 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis## 2024-12-18 17:45:06.992188 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified## 2024-12-18 17:45:07.237978 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii## 2024-12-18 17:45:07.470153 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum## 2024-12-18 17:45:07.716159 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis## 2024-12-18 17:45:07.94836 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis## 2024-12-18 17:45:08.193174 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila## 2024-12-18 17:45:08.425766 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis## 2024-12-18 17:45:08.664978 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified## 2024-12-18 17:45:08.903964 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum## 2024-12-18 17:45:09.137881 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii## 2024-12-18 17:45:09.384505 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified## 2024-12-18 17:45:09.620625 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris## 2024-12-18 17:45:09.864838 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus## 2024-12-18 17:45:10.092755 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus## 2024-12-18 17:45:10.329905 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis## 2024-12-18 17:45:10.567263 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale## 2024-12-18 17:45:10.847238 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus## 2024-12-18 17:45:11.085641 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis## 2024-12-18 17:45:11.331302 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale## 2024-12-18 17:45:11.564099 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii## 2024-12-18 17:45:11.812278 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus## 2024-12-18 17:45:12.042143 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii## 2024-12-18 17:45:12.282823 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis## 2024-12-18 17:45:12.514761 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae## 2024-12-18 17:45:12.760108 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.siraeumSession info from running the demo in R can be displayed with the following command.
sessionInfo()## R Under development (unstable) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] Maaslin2_1.21.0
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.9 generics_0.1.3 robustbase_0.99-4-1
## [4] lattice_0.22-6 lme4_1.1-35.5 digest_0.6.37
## [7] magrittr_2.0.3 RColorBrewer_1.1-3 evaluate_1.0.1
## [10] grid_4.5.0 mvtnorm_1.3-2 fastmap_1.2.0
## [13] jsonlite_1.8.9 Matrix_1.7-1 DBI_1.2.3
## [16] optparse_1.7.5 biglm_0.9-3 mgcv_1.9-1
## [19] scales_1.3.0 pbapply_1.7-2 permute_0.9-7
## [22] numDeriv_2016.8-1.1 getopt_1.20.4 jquerylib_0.1.4
## [25] cli_3.6.3 rlang_1.1.4 crayon_1.5.3
## [28] munsell_0.5.1 splines_4.5.0 withr_3.0.2
## [31] cachem_1.1.0 yaml_2.3.10 vegan_2.6-8
## [34] tools_4.5.0 parallel_4.5.0 nloptr_2.1.1
## [37] minqa_1.2.8 dplyr_1.1.4 colorspace_2.1-1
## [40] ggplot2_3.5.1 boot_1.3-31 hash_2.2.6.3
## [43] vctrs_0.6.5 R6_2.5.1 lifecycle_1.0.4
## [46] MASS_7.3-61 logging_0.10-108 pcaPP_2.0-5
## [49] cluster_2.1.8 pkgconfig_2.0.3 gtable_0.3.6
## [52] lmerTest_3.1-3 pillar_1.10.0 bslib_0.8.0
## [55] Rcpp_1.0.13-1 data.table_1.16.4 glue_1.8.0
## [58] DEoptimR_1.1-3-1 xfun_0.49 tibble_3.2.1
## [61] tidyselect_1.2.1 knitr_1.49 farver_2.1.2
## [64] htmltools_0.5.8.1 nlme_3.1-166 labeling_0.4.3
## [67] rmarkdown_2.29 pheatmap_1.0.12 compiler_4.5.0Run 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?