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"
## 2024-04-17 17:45:59.975829 INFO::Writing function arguments to log file
## 2024-04-17 17:46:00.006448 INFO::Verifying options selected are valid
## 2024-04-17 17:46:00.040294 INFO::Determining format of input files
## 2024-04-17 17:46:00.041394 INFO::Input format is data samples as rows and metadata samples as rows
## 2024-04-17 17:46:00.045329 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2024-04-17 17:46:00.046382 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2024-04-17 17:46:00.048592 INFO::Filter data based on min abundance and min prevalence
## 2024-04-17 17:46:00.04923 INFO::Total samples in data: 1595
## 2024-04-17 17:46:00.049829 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2024-04-17 17:46:00.054467 INFO::Total filtered features: 0
## 2024-04-17 17:46:00.055227 INFO::Filtered feature names from abundance and prevalence filtering:
## 2024-04-17 17:46:00.064043 INFO::Total filtered features with variance filtering: 0
## 2024-04-17 17:46:00.064761 INFO::Filtered feature names from variance filtering:
## 2024-04-17 17:46:00.065359 INFO::Running selected normalization method: TSS
## 2024-04-17 17:46:01.127519 INFO::Bypass z-score application to metadata
## 2024-04-17 17:46:01.128519 INFO::Running selected transform method: LOG
## 2024-04-17 17:46:01.143601 INFO::Running selected analysis method: LM
## 2024-04-17 17:46:01.421351 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:01.744984 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2024-04-17 17:46:01.961861 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2024-04-17 17:46:02.29491 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:02.425959 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2024-04-17 17:46:02.581839 INFO::Fitting model to feature number 6, Bacteroides.caccae## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:02.731304 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2024-04-17 17:46:02.877827 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2024-04-17 17:46:03.020736 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2024-04-17 17:46:03.155751 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2024-04-17 17:46:03.300298 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## 2024-04-17 17:46:03.444812 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## 2024-04-17 17:46:03.59858 INFO::Fitting model to feature number 12, Bacteroides.fragilis## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:03.746788 INFO::Fitting model to feature number 13, Bacteroides.intestinalis## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:03.89835 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2024-04-17 17:46:04.038091 INFO::Fitting model to feature number 15, Bacteroides.ovatus## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:04.17571 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2024-04-17 17:46:04.34908 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2024-04-17 17:46:04.590053 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:04.762983 INFO::Fitting model to feature number 19, Bacteroides.uniformis## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:04.909948 INFO::Fitting model to feature number 20, Bacteroides.vulgatus## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:05.066728 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:05.20591 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2024-04-17 17:46:05.348318 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2024-04-17 17:46:05.496652 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2024-04-17 17:46:05.691489 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2024-04-17 17:46:05.858039 INFO::Fitting model to feature number 26, Parabacteroides.distasonis## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:06.056314 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2024-04-17 17:46:06.216129 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2024-04-17 17:46:06.361332 INFO::Fitting model to feature number 29, Parabacteroides.unclassified## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:06.50429 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2024-04-17 17:46:06.640583 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2024-04-17 17:46:06.778182 INFO::Fitting model to feature number 32, Prevotella.copri## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:06.918109 INFO::Fitting model to feature number 33, Alistipes.finegoldii## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:07.052304 INFO::Fitting model to feature number 34, Alistipes.onderdonkii## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:07.200619 INFO::Fitting model to feature number 35, Alistipes.putredinis## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:07.356102 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2024-04-17 17:46:07.499752 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2024-04-17 17:46:07.633846 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2024-04-17 17:46:07.771036 INFO::Fitting model to feature number 39, Clostridium.bolteae## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:07.910741 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## 2024-04-17 17:46:08.030259 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## 2024-04-17 17:46:08.167587 INFO::Fitting model to feature number 41, Clostridium.clostridioforme## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:08.308791 INFO::Fitting model to feature number 42, Clostridium.hathewayi## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:08.439571 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2024-04-17 17:46:08.590576 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2024-04-17 17:46:08.72313 INFO::Fitting model to feature number 45, Clostridium.symbiosum## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:08.860659 INFO::Fitting model to feature number 46, Flavonifractor.plautii## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:08.996753 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2024-04-17 17:46:09.160956 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2024-04-17 17:46:09.312801 INFO::Fitting model to feature number 49, Eubacterium.rectale## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:09.465233 INFO::Fitting model to feature number 50, Eubacterium.siraeum## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:09.595199 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:09.733588 INFO::Fitting model to feature number 52, Eubacterium.ventriosum## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:09.862641 INFO::Fitting model to feature number 53, Ruminococcus.gnavus## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:09.996762 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2024-04-17 17:46:10.132092 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2024-04-17 17:46:10.508501 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2024-04-17 17:46:10.642512 INFO::Fitting model to feature number 57, Dorea.longicatena## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:10.775913 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:10.917263 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:11.049609 INFO::Fitting model to feature number 60, Roseburia.hominis## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:11.182962 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2024-04-17 17:46:11.308527 INFO::Fitting model to feature number 62, Roseburia.inulinivorans## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:11.446394 INFO::Fitting model to feature number 63, Roseburia.unclassified## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:11.579002 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2024-04-17 17:46:11.741891 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2024-04-17 17:46:11.901231 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2024-04-17 17:46:12.036655 INFO::Fitting model to feature number 67, Ruminococcus.bromii## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:12.16835 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2024-04-17 17:46:12.306283 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2024-04-17 17:46:12.444434 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:12.577618 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2024-04-17 17:46:12.713645 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2024-04-17 17:46:12.850631 INFO::Fitting model to feature number 73, Dialister.invisus## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:12.978747 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2024-04-17 17:46:13.129581 INFO::Fitting model to feature number 75, Veillonella.dispar## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:13.265065 INFO::Fitting model to feature number 76, Veillonella.parvula## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:13.396229 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2024-04-17 17:46:13.737686 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2024-04-17 17:46:13.871798 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2024-04-17 17:46:14.000868 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2024-04-17 17:46:14.137619 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2024-04-17 17:46:14.286307 INFO::Fitting model to feature number 82, Escherichia.coli
## 2024-04-17 17:46:14.421168 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2024-04-17 17:46:14.544251 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:14.677966 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae## boundary (singular) fit: see help('isSingular')## 2024-04-17 17:46:14.811441 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2024-04-17 17:46:14.959166 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2024-04-17 17:46:15.154125 INFO::Counting total values for each feature
## 2024-04-17 17:46:15.185803 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2024-04-17 17:46:15.328807 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2024-04-17 17:46:15.476986 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2024-04-17 17:46:15.708917 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2024-04-17 17:46:15.77132 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2024-04-17 17:46:15.806783 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2024-04-17 17:46:15.812242 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2024-04-17 17:46:15.81863 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
## 2024-04-17 17:46:15.821574 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2024-04-17 17:46:16.044225 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2024-04-17 17:46:16.058172 INFO::Plotting associations from most to least significant, grouped by metadata
## 2024-04-17 17:46:16.059052 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2024-04-17 17:46:16.060428 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii## 2024-04-17 17:46:16.384983 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified## 2024-04-17 17:46:16.662444 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis## 2024-04-17 17:46:16.907074 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale## 2024-04-17 17:46:17.167956 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus## 2024-04-17 17:46:17.40128 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus## 2024-04-17 17:46:17.643848 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum## 2024-04-17 17:46:17.875269 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified## 2024-04-17 17:46:18.113276 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans## 2024-04-17 17:46:18.346063 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis## 2024-04-17 17:46:18.58427 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron## 2024-04-17 17:46:18.819459 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis## 2024-04-17 17:46:19.057587 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis## 2024-04-17 17:46:19.295162 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei## 2024-04-17 17:46:19.551233 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii## 2024-04-17 17:46:19.791195 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens## 2024-04-17 17:46:20.034415 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum## 2024-04-17 17:46:20.262781 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena## 2024-04-17 17:46:20.500306 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae## 2024-04-17 17:46:20.730014 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-04-17 17:46:20.969784 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli## 2024-04-17 17:46:21.201504 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae## 2024-04-17 17:46:21.441289 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified## 2024-04-17 17:46:21.667281 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii## 2024-04-17 17:46:21.925546 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens## 2024-04-17 17:46:22.159852 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris## 2024-04-17 17:46:22.397076 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes## 2024-04-17 17:46:22.62509 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis## 2024-04-17 17:46:22.91934 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii## 2024-04-17 17:46:23.153708 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii## 2024-04-17 17:46:23.397088 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis## 2024-04-17 17:46:23.634622 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara## 2024-04-17 17:46:23.874946 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum## 2024-04-17 17:46:24.101751 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae## 2024-04-17 17:46:24.337687 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified## 2024-04-17 17:46:24.575413 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens## 2024-04-17 17:46:24.828921 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus## 2024-04-17 17:46:25.092172 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme## 2024-04-17 17:46:25.35232 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii## 2024-04-17 17:46:25.5916 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii## 2024-04-17 17:46:25.836947 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum## 2024-04-17 17:46:26.082034 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris## 2024-04-17 17:46:26.329998 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47## 2024-04-17 17:46:26.555687 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus## 2024-04-17 17:46:26.797531 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii## 2024-04-17 17:46:27.030379 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis## 2024-04-17 17:46:27.263551 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified## 2024-04-17 17:46:27.494979 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques## 2024-04-17 17:46:27.725465 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified## 2024-04-17 17:46:27.96653 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus## 2024-04-17 17:46:28.227336 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis## 2024-04-17 17:46:28.457254 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified## 2024-04-17 17:46:28.698246 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified## 2024-04-17 17:46:28.929582 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis## 2024-04-17 17:46:29.159655 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis## 2024-04-17 17:46:29.389737 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31## 2024-04-17 17:46:29.628934 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae## 2024-04-17 17:46:29.852575 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8## 2024-04-17 17:46:30.082797 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae## 2024-04-17 17:46:30.312865 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii## 2024-04-17 17:46:30.545466 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii## 2024-04-17 17:46:30.779568 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum## 2024-04-17 17:46:31.014296 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA## 2024-04-17 17:46:34.030914 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2024-04-17 17:46:34.032773 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified## 2024-04-17 17:46:34.250784 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii## 2024-04-17 17:46:34.48915 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae## 2024-04-17 17:46:34.740712 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified## 2024-04-17 17:46:34.977562 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis## 2024-04-17 17:46:35.232036 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum## 2024-04-17 17:46:35.474143 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus## 2024-04-17 17:46:35.717008 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis## 2024-04-17 17:46:35.95469 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii## 2024-04-17 17:46:36.20924 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale## 2024-04-17 17:46:36.456381 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis## 2024-04-17 17:46:36.725239 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis## 2024-04-17 17:46:36.958248 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-04-17 17:46:37.206288 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii## 2024-04-17 17:46:37.440394 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens## 2024-04-17 17:46:37.688637 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris## 2024-04-17 17:46:37.928483 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii## 2024-04-17 17:46:38.184245 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis## 2024-04-17 17:46:38.41545 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum## 2024-04-17 17:46:38.663135 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus## 2024-04-17 17:46:38.89373 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii## 2024-04-17 17:46:39.143143 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii## 2024-04-17 17:46:39.37934 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae## 2024-04-17 17:46:39.628497 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus## 2024-04-17 17:46:39.861967 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum## 2024-04-17 17:46:40.106728 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae## 2024-04-17 17:46:40.343874 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae## 2024-04-17 17:46:40.580748 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum## 2024-04-17 17:46:40.809953 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis## 2024-04-17 17:46:41.053089 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii## 2024-04-17 17:46:41.292172 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques## 2024-04-17 17:46:41.525871 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8## 2024-04-17 17:46:41.80386 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum## 2024-04-17 17:46:42.038393 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum## 2024-04-17 17:46:42.29321 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis## 2024-04-17 17:46:42.520795 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens## 2024-04-17 17:46:42.765413 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi## 2024-04-17 17:46:42.998325 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified## 2024-04-17 17:46:43.290027 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens## 2024-04-17 17:46:43.528286 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus## 2024-04-17 17:46:43.781053 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae## 2024-04-17 17:46:44.023043 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus## 2024-04-17 17:46:44.278516 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris## 2024-04-17 17:46:44.519587 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47## 2024-04-17 17:46:47.522995 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2024-04-17 17:46:47.52485 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii## 2024-04-17 17:46:47.742157 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale## 2024-04-17 17:46:47.983727 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31## 2024-04-17 17:46:48.23592 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis## 2024-04-17 17:46:48.466162 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified## 2024-04-17 17:46:48.720412 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-04-17 17:46:48.961128 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques## 2024-04-17 17:46:49.21119 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum## 2024-04-17 17:46:49.452054 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus## 2024-04-17 17:46:49.699766 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli## 2024-04-17 17:46:49.933266 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum## 2024-04-17 17:46:50.187907 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified## 2024-04-17 17:46:50.428035 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis## 2024-04-17 17:46:50.678875 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens## 2024-04-17 17:46:50.928738 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae## 2024-04-17 17:46:51.173424 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii## 2024-04-17 17:46:51.414396 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus## 2024-04-17 17:46:51.647771 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified## 2024-04-17 17:46:51.900723 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis## 2024-04-17 17:46:52.133868 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii## 2024-04-17 17:46:52.384595 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans## 2024-04-17 17:46:52.622737 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii## 2024-04-17 17:46:52.876642 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified## 2024-04-17 17:46:53.113505 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii## 2024-04-17 17:46:53.360258 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis## 2024-04-17 17:46:53.598242 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri## 2024-04-17 17:46:54.160436 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei## 2024-04-17 17:46:54.387581 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis## 2024-04-17 17:46:54.62129 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii## 2024-04-17 17:46:57.477492 INFO::Plotting data for metadata number 4, antibiotics
## 2024-04-17 17:46:57.479167 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans## 2024-04-17 17:46:57.667479 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis## 2024-04-17 17:46:57.894866 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale## 2024-04-17 17:46:58.113806 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus## 2024-04-17 17:46:58.346671 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis## 2024-04-17 17:46:58.559412 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena## 2024-04-17 17:46:58.777211 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus## 2024-04-17 17:46:58.998347 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii## 2024-04-17 17:46:59.209803 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum## 2024-04-17 17:46:59.430322 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae## 2024-04-17 17:46:59.675368 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis## 2024-04-17 17:46:59.917629 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii## 2024-04-17 17:47:00.147356 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii## 2024-04-17 17:47:00.38324 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified## 2024-04-17 17:47:00.599154 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum## 2024-04-17 17:47:00.847515 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-04-17 17:47:01.068044 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii## 2024-04-17 17:47:01.297164 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31## 2024-04-17 17:47:01.507778 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis## 2024-04-17 17:47:01.728006 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii## 2024-04-17 17:47:01.942223 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis## 2024-04-17 17:47:02.168963 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens## 2024-04-17 17:47:02.378532 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens## 2024-04-17 17:47:02.597242 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron## 2024-04-17 17:47:02.816062 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii## 2024-04-17 17:47:03.03481 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae## 2024-04-17 17:47:03.247621 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum## 2024-04-17 17:47:03.464422 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques## 2024-04-17 17:47:03.67749 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum## 2024-04-17 17:47:03.90223 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis## 2024-04-17 17:47:04.124777 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified## 2024-04-17 17:47:04.344193 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar## 2024-04-17 17:47:04.562938 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica## 2024-04-17 17:47:04.777267 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8## 2024-04-17 17:47:04.994578 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile## 2024-04-17 17:47:05.208239 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47## 2024-04-17 17:47:05.475121 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA## 2024-04-17 17:47:05.696257 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila## 2024-04-17 17:47:05.925057 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae## 2024-04-17 17:47:06.140192 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus## 2024-04-17 17:47:08.875582 INFO::Plotting data for metadata number 5, age
## 2024-04-17 17:47:08.87727 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()`).## 2024-04-17 17:47:09.126588 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()`).## 2024-04-17 17:47:09.438663 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()`).## 2024-04-17 17:47:09.678451 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()`).## 2024-04-17 17:47:09.938689 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()`).## 2024-04-17 17:47:10.189616 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()`).## 2024-04-17 17:47:10.418186 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()`).## 2024-04-17 17:47:10.653429 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()`).## 2024-04-17 17:47:10.885362 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()`).## 2024-04-17 17:47:11.106663 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()`).## 2024-04-17 17:47:11.33934 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()`).## 2024-04-17 17:47:11.554802 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()`).## 2024-04-17 17:47:11.783358 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()`).## 2024-04-17 17:47:12.015864 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()`).## 2024-04-17 17:47:12.231622 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()`).## 2024-04-17 17:47:12.454633 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()`).## 2024-04-17 17:47:12.672101 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()`).## 2024-04-17 17:47:12.897818 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()`).## 2024-04-17 17:47:13.121772 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()`).## 2024-04-17 17:47:13.34042 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()`).## 2024-04-17 17:47:13.576265 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()`).## 2024-04-17 17:47:13.803834 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()`).## 2024-04-17 17:47:16.711468 INFO::Plotting data for metadata number 6, diagnosis
## 2024-04-17 17:47:16.713313 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis## 2024-04-17 17:47:16.92986 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila## 2024-04-17 17:47:17.158334 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae## 2024-04-17 17:47:17.402121 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis## 2024-04-17 17:47:17.634948 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified## 2024-04-17 17:47:17.882005 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme## 2024-04-17 17:47:18.114182 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii## 2024-04-17 17:47:18.359525 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii## 2024-04-17 17:47:18.593506 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum## 2024-04-17 17:47:18.849504 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum## 2024-04-17 17:47:19.099962 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans## 2024-04-17 17:47:19.355202 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii## 2024-04-17 17:47:19.602998 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii## 2024-04-17 17:47:19.843235 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii## 2024-04-17 17:47:20.09701 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii## 2024-04-17 17:47:20.33413 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified## 2024-04-17 17:47:20.582385 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum## 2024-04-17 17:47:20.829056 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis## 2024-04-17 17:47:21.0793 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified## 2024-04-17 17:47:21.316977 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii## 2024-04-17 17:47:21.567261 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum## 2024-04-17 17:47:21.805825 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis## 2024-04-17 17:47:22.067944 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis## 2024-04-17 17:47:22.325139 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila## 2024-04-17 17:47:22.561247 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis## 2024-04-17 17:47:22.808128 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified## 2024-04-17 17:47:23.040468 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum## 2024-04-17 17:47:23.309235 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii## 2024-04-17 17:47:23.546102 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified## 2024-04-17 17:47:23.801094 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris## 2024-04-17 17:47:24.04903 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus## 2024-04-17 17:47:24.282481 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus## 2024-04-17 17:47:24.572668 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis## 2024-04-17 17:47:24.8146 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale## 2024-04-17 17:47:25.073972 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus## 2024-04-17 17:47:25.319891 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis## 2024-04-17 17:47:25.569558 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale## 2024-04-17 17:47:25.807559 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii## 2024-04-17 17:47:26.065906 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus## 2024-04-17 17:47:26.298708 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii## 2024-04-17 17:47:26.545442 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis## 2024-04-17 17:47:26.781819 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae## 2024-04-17 17:47:27.03284 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 version 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## 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_1.17.0
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.4 biglm_0.9-2.1 xfun_0.43
## [4] bslib_0.7.0 ggplot2_3.5.0 lattice_0.22-6
## [7] numDeriv_2016.8-1.1 vctrs_0.6.5 tools_4.4.0
## [10] generics_0.1.3 parallel_4.4.0 getopt_1.20.4
## [13] tibble_3.2.1 fansi_1.0.6 DEoptimR_1.1-3
## [16] cluster_2.1.6 pkgconfig_2.0.3 logging_0.10-108
## [19] pheatmap_1.0.12 Matrix_1.7-0 data.table_1.15.4
## [22] RColorBrewer_1.1-3 lifecycle_1.0.4 farver_2.1.1
## [25] compiler_4.4.0 munsell_0.5.1 lmerTest_3.1-3
## [28] permute_0.9-7 htmltools_0.5.8.1 sass_0.4.9
## [31] hash_2.2.6.3 yaml_2.3.8 pillar_1.9.0
## [34] nloptr_2.0.3 crayon_1.5.2 jquerylib_0.1.4
## [37] MASS_7.3-60.2 cachem_1.0.8 vegan_2.6-4
## [40] boot_1.3-30 nlme_3.1-164 robustbase_0.99-2
## [43] tidyselect_1.2.1 digest_0.6.35 mvtnorm_1.2-4
## [46] dplyr_1.1.4 labeling_0.4.3 splines_4.4.0
## [49] pcaPP_2.0-4 fastmap_1.1.1 grid_4.4.0
## [52] colorspace_2.1-0 cli_3.6.2 magrittr_2.0.3
## [55] utf8_1.2.4 withr_3.0.0 scales_1.3.0
## [58] rmarkdown_2.26 lme4_1.1-35.3 pbapply_1.7-2
## [61] evaluate_0.23 knitr_1.46 mgcv_1.9-1
## [64] rlang_1.1.3 Rcpp_1.0.12 glue_1.7.0
## [67] optparse_1.7.5 DBI_1.2.2 minqa_1.2.6
## [70] jsonlite_1.8.8 R6_2.5.1Run 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?