MaAsLin2 is the next generation of MaAsLin (Microbiome Multivariable Association with Linear Models).
MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta-omics features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, along with a variety of filtering, normalization, and transform methods.
If you use the MaAsLin2 software, please cite our manuscript:
Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C (2021). Multivariable Association Discovery in Population-scale Meta-omics Studies. PLoS Computational Biology, 17(11):e1009442.
Check out the MaAsLin 2 tutorial for an overview of analysis options.
If you have questions, please direct it to :
MaAsLin2 Forum
Google Groups (Read only)
MaAsLin2 finds associations between microbiome multi-omics features and complex metadata in population-scale epidemiological studies. The software includes multiple analysis methods (with support for multiple covariates and repeated measures), filtering, normalization, and transform options to customize analysis for your specific study.
MaAsLin2 is an R package that can be run on the command line or as an R function.
MaAsLin2 can be run from the command line or as an R function. If only running from the command line, you do not need to install the MaAsLin2 package but you will need to install the MaAsLin2 dependencies.
$ tar xzvf maaslin2.tar.gz
$ R -q -e "install.packages(c('lmerTest','pbapply','car','dplyr','vegan','chemometrics','ggplot2','pheatmap','hash','logging','data.table','glmmTMB','MASS','cplm','pscl'), repos='http://cran.r-project.org')"
$ R CMD INSTALL maaslin2
Install Bioconductor and then install Maaslin2
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Maaslin2")
MaAsLin2 can be run from the command line or as an R function. Both methods require the same arguments, have the same options, and use the same default settings.
MaAsLin2 requires two input files.
The data file can contain samples not included in the metadata file (along with the reverse case). For both cases, those samples not included in both files will be removed from the analysis. Also the samples do not need to be in the same order in the two files.
NOTE: If running MaAsLin2 as a function, the data and metadata inputs can be of type data.frame
instead of a path to a file.
MaAsLin2 generates two types of output files: data and visualization.
all_results.tsv
N
column is the total number of data points.N.not.zero
column is the total of non-zero data points.p.adjust
with the correction method.significant_results.tsv
models.rds
residuals.rds
fitted.rds
ranef.rds
maaslin2.log
heatmap.pdf
[a-z/0-9]+.pdf
Example input files can be found in the inst/extdata
folder of the MaAsLin2 source. The files provided were generated from the HMP2 data which can be downloaded from https://ibdmdb.org/ .
HMP2_taxonomy.tsv
: is a tab-demilited file with species as columns and samples as rows. It is a subset of the taxonomy file so it just includes the species abundances for all samples.
HMP2_metadata.tsv
: is a tab-delimited file with samples as rows and metadata as columns. It is a subset of the metadata file so that it just includes some of the fields.
$ Maaslin2.R --fixed_effects="diagnosis,dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age" --random_effects="site,subject" --standardize=FALSE inst/extdata/HMP2_taxonomy.tsv inst/extdata/HMP2_metadata.tsv demo_output
HMP2_taxonomy.tsv
is the path to your data (or features) fileHMP2_metadata.tsv
is the path to your metadata filedemo_output
is the path to the folder to write the outputlibrary(Maaslin2)
input_data <- system.file(
'extdata','HMP2_taxonomy.tsv', package="Maaslin2")
input_metadata <-system.file(
'extdata','HMP2_metadata.tsv', package="Maaslin2")
fit_data <- Maaslin2(
input_data, input_metadata, 'demo_output',
fixed_effects = c('diagnosis', 'dysbiosisnonIBD','dysbiosisUC','dysbiosisCD', 'antibiotics', 'age'),
random_effects = c('site', 'subject'),
reference = "diagnosis,nonIBD",
standardize = FALSE)
## [1] "Creating output folder"
## [1] "Creating output feature tables folder"
## [1] "Creating output fits folder"
## [1] "Creating output figures folder"
## 2024-04-30 23:56:00.550168 INFO::Writing function arguments to log file
## 2024-04-30 23:56:00.581595 INFO::Verifying options selected are valid
## 2024-04-30 23:56:00.636497 INFO::Determining format of input files
## 2024-04-30 23:56:00.638262 INFO::Input format is data samples as rows and metadata samples as rows
## 2024-04-30 23:56:00.646742 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2024-04-30 23:56:00.648567 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2024-04-30 23:56:00.652232 INFO::Filter data based on min abundance and min prevalence
## 2024-04-30 23:56:00.653217 INFO::Total samples in data: 1595
## 2024-04-30 23:56:00.654296 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2024-04-30 23:56:00.660357 INFO::Total filtered features: 0
## 2024-04-30 23:56:00.661825 INFO::Filtered feature names from abundance and prevalence filtering:
## 2024-04-30 23:56:00.671821 INFO::Total filtered features with variance filtering: 0
## 2024-04-30 23:56:00.672847 INFO::Filtered feature names from variance filtering:
## 2024-04-30 23:56:00.673611 INFO::Running selected normalization method: TSS
## 2024-04-30 23:56:01.917561 INFO::Bypass z-score application to metadata
## 2024-04-30 23:56:01.918603 INFO::Running selected transform method: LOG
## 2024-04-30 23:56:01.94181 INFO::Running selected analysis method: LM
## 2024-04-30 23:56:02.315642 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:02.67106 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2024-04-30 23:56:02.838616 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2024-04-30 23:56:03.012489 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:03.247149 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2024-04-30 23:56:03.423116 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:03.57726 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2024-04-30 23:56:03.733914 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2024-04-30 23:56:03.892561 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2024-04-30 23:56:04.065972 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2024-04-30 23:56:04.2394 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
## 2024-04-30 23:56:04.369664 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
## 2024-04-30 23:56:04.533165 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:04.672994 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:04.837065 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2024-04-30 23:56:04.991517 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:05.147289 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2024-04-30 23:56:05.282165 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2024-04-30 23:56:05.441435 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:05.592521 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:05.724445 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:05.867644 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:06.00718 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2024-04-30 23:56:06.161475 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2024-04-30 23:56:06.339695 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2024-04-30 23:56:06.489727 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2024-04-30 23:56:06.623114 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:06.769258 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2024-04-30 23:56:06.912809 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2024-04-30 23:56:07.044441 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:07.212875 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2024-04-30 23:56:07.369835 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2024-04-30 23:56:07.525727 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:07.645135 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:07.799765 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:07.962929 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:08.116557 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2024-04-30 23:56:08.480277 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2024-04-30 23:56:08.631179 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2024-04-30 23:56:08.793987 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:09.146572 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
## 2024-04-30 23:56:09.275951 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
## 2024-04-30 23:56:09.422354 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:09.565826 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:09.687415 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2024-04-30 23:56:09.810269 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2024-04-30 23:56:09.92965 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:10.067043 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:10.181229 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2024-04-30 23:56:10.310472 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2024-04-30 23:56:10.462398 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:10.600807 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:10.728385 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:10.866238 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:10.976308 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:11.125345 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2024-04-30 23:56:11.251632 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2024-04-30 23:56:11.369437 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2024-04-30 23:56:11.497017 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:11.630905 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:11.76868 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:11.932032 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:12.063867 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2024-04-30 23:56:12.17967 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:12.333819 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:12.486265 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2024-04-30 23:56:12.634953 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2024-04-30 23:56:12.782016 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2024-04-30 23:56:12.917314 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:13.061309 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2024-04-30 23:56:13.217657 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2024-04-30 23:56:13.376177 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:13.511585 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2024-04-30 23:56:13.657527 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2024-04-30 23:56:13.816297 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:13.947102 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2024-04-30 23:56:14.071598 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:14.201302 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:14.312043 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2024-04-30 23:56:14.439989 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2024-04-30 23:56:14.571729 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2024-04-30 23:56:14.707349 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2024-04-30 23:56:14.86675 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2024-04-30 23:56:15.019368 INFO::Fitting model to feature number 82, Escherichia.coli
## 2024-04-30 23:56:15.154895 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2024-04-30 23:56:15.278296 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:15.419316 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 23:56:15.553405 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2024-04-30 23:56:15.71151 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2024-04-30 23:56:15.907974 INFO::Counting total values for each feature
## 2024-04-30 23:56:15.933782 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2024-04-30 23:56:16.06213 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2024-04-30 23:56:16.205113 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2024-04-30 23:56:16.415182 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2024-04-30 23:56:16.472844 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2024-04-30 23:56:16.50535 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2024-04-30 23:56:16.511967 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2024-04-30 23:56:16.518959 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
## 2024-04-30 23:56:16.522854 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2024-04-30 23:56:16.701048 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2024-04-30 23:56:16.709918 INFO::Plotting associations from most to least significant, grouped by metadata
## 2024-04-30 23:56:16.711608 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2024-04-30 23:56:16.713656 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2024-04-30 23:56:17.101172 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2024-04-30 23:56:17.401026 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2024-04-30 23:56:17.696088 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2024-04-30 23:56:17.986636 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2024-04-30 23:56:18.264536 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2024-04-30 23:56:18.551353 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2024-04-30 23:56:18.814942 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2024-04-30 23:56:19.098893 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2024-04-30 23:56:19.378489 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2024-04-30 23:56:19.644651 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2024-04-30 23:56:19.933592 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2024-04-30 23:56:20.212146 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2024-04-30 23:56:20.511681 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2024-04-30 23:56:20.762481 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2024-04-30 23:56:21.061363 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2024-04-30 23:56:21.367286 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2024-04-30 23:56:21.661146 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2024-04-30 23:56:21.932449 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2024-04-30 23:56:22.236257 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-04-30 23:56:22.493935 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2024-04-30 23:56:22.780083 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2024-04-30 23:56:23.070654 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2024-04-30 23:56:23.310461 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2024-04-30 23:56:23.569682 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2024-04-30 23:56:23.849632 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2024-04-30 23:56:24.093723 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2024-04-30 23:56:24.382189 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2024-04-30 23:56:24.639216 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2024-04-30 23:56:24.872644 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2024-04-30 23:56:25.157562 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2024-04-30 23:56:25.39802 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2024-04-30 23:56:25.672823 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2024-04-30 23:56:25.937687 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2024-04-30 23:56:26.21957 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2024-04-30 23:56:26.502609 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2024-04-30 23:56:26.785943 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2024-04-30 23:56:27.065308 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2024-04-30 23:56:27.329788 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2024-04-30 23:56:27.605716 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2024-04-30 23:56:27.885753 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2024-04-30 23:56:28.247672 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2024-04-30 23:56:28.516631 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2024-04-30 23:56:28.809635 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2024-04-30 23:56:29.089779 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2024-04-30 23:56:29.354018 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2024-04-30 23:56:29.649132 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2024-04-30 23:56:29.968358 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2024-04-30 23:56:30.241921 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2024-04-30 23:56:30.535206 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2024-04-30 23:56:30.811097 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2024-04-30 23:56:31.094929 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2024-04-30 23:56:31.337729 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2024-04-30 23:56:31.611237 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2024-04-30 23:56:31.890614 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2024-04-30 23:56:32.193049 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2024-04-30 23:56:32.483519 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2024-04-30 23:56:32.759966 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2024-04-30 23:56:33.019587 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2024-04-30 23:56:33.285777 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2024-04-30 23:56:33.576831 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2024-04-30 23:56:33.868806 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2024-04-30 23:56:34.135592 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-04-30 23:56:37.070329 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2024-04-30 23:56:37.07263 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2024-04-30 23:56:37.311799 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2024-04-30 23:56:37.614106 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2024-04-30 23:56:37.893062 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2024-04-30 23:56:38.183262 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2024-04-30 23:56:38.505006 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2024-04-30 23:56:38.788016 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2024-04-30 23:56:39.084957 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2024-04-30 23:56:39.376285 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2024-04-30 23:56:39.717265 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2024-04-30 23:56:39.981389 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2024-04-30 23:56:40.230695 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2024-04-30 23:56:40.476805 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-04-30 23:56:40.77091 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2024-04-30 23:56:41.033203 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2024-04-30 23:56:41.327822 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2024-04-30 23:56:41.554941 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2024-04-30 23:56:41.832034 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2024-04-30 23:56:42.110067 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2024-04-30 23:56:42.353951 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2024-04-30 23:56:42.630021 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2024-04-30 23:56:42.894474 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2024-04-30 23:56:43.159029 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2024-04-30 23:56:43.428039 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2024-04-30 23:56:43.712256 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2024-04-30 23:56:43.982387 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2024-04-30 23:56:44.231653 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2024-04-30 23:56:44.462067 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2024-04-30 23:56:44.722829 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2024-04-30 23:56:44.997187 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2024-04-30 23:56:45.325045 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2024-04-30 23:56:45.610226 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2024-04-30 23:56:45.910383 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2024-04-30 23:56:46.138363 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2024-04-30 23:56:46.432187 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2024-04-30 23:56:46.718319 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2024-04-30 23:56:47.001205 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2024-04-30 23:56:47.318496 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2024-04-30 23:56:47.599713 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2024-04-30 23:56:47.930859 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2024-04-30 23:56:48.259702 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2024-04-30 23:56:48.584292 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2024-04-30 23:56:48.854498 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2024-04-30 23:56:49.144702 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2024-04-30 23:56:52.143642 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2024-04-30 23:56:52.145873 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2024-04-30 23:56:52.412171 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2024-04-30 23:56:52.703323 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2024-04-30 23:56:53.004499 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2024-04-30 23:56:53.268085 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2024-04-30 23:56:53.565912 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-04-30 23:56:53.842684 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2024-04-30 23:56:54.126578 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2024-04-30 23:56:54.399098 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2024-04-30 23:56:54.634537 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2024-04-30 23:56:54.880507 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2024-04-30 23:56:55.13708 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2024-04-30 23:56:55.40745 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2024-04-30 23:56:55.661745 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2024-04-30 23:56:55.929096 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2024-04-30 23:56:56.180818 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2024-04-30 23:56:56.446813 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2024-04-30 23:56:56.720299 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2024-04-30 23:56:57.01843 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2024-04-30 23:56:57.285771 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2024-04-30 23:56:57.531676 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2024-04-30 23:56:57.790219 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2024-04-30 23:56:58.071812 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2024-04-30 23:56:58.363705 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2024-04-30 23:56:58.625395 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2024-04-30 23:56:58.897719 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2024-04-30 23:56:59.136223 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2024-04-30 23:56:59.421217 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2024-04-30 23:56:59.699057 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2024-04-30 23:57:02.658838 INFO::Plotting data for metadata number 4, antibiotics
## 2024-04-30 23:57:02.661563 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2024-04-30 23:57:02.870707 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2024-04-30 23:57:03.101358 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2024-04-30 23:57:03.339471 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2024-04-30 23:57:03.589073 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2024-04-30 23:57:03.845971 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2024-04-30 23:57:04.105886 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2024-04-30 23:57:04.336112 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2024-04-30 23:57:04.566971 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2024-04-30 23:57:04.783369 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2024-04-30 23:57:05.032765 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2024-04-30 23:57:05.233463 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2024-04-30 23:57:05.497321 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2024-04-30 23:57:05.768843 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2024-04-30 23:57:06.026216 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2024-04-30 23:57:06.283311 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-04-30 23:57:06.521481 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2024-04-30 23:57:06.761166 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2024-04-30 23:57:06.985569 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2024-04-30 23:57:07.228339 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2024-04-30 23:57:07.47292 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2024-04-30 23:57:07.727133 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2024-04-30 23:57:07.960563 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2024-04-30 23:57:08.210391 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2024-04-30 23:57:08.466467 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2024-04-30 23:57:08.730918 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2024-04-30 23:57:08.974345 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2024-04-30 23:57:09.223675 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2024-04-30 23:57:09.451438 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2024-04-30 23:57:09.699179 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2024-04-30 23:57:09.906735 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2024-04-30 23:57:10.149884 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2024-04-30 23:57:10.358852 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2024-04-30 23:57:10.603891 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2024-04-30 23:57:10.83862 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2024-04-30 23:57:11.054973 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2024-04-30 23:57:11.272568 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-04-30 23:57:11.510851 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2024-04-30 23:57:11.735467 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2024-04-30 23:57:11.970429 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2024-04-30 23:57:14.50091 INFO::Plotting data for metadata number 5, age
## 2024-04-30 23:57:14.503183 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()`).
## 2024-04-30 23:57:14.743541 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()`).
## 2024-04-30 23:57:15.056517 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()`).
## 2024-04-30 23:57:15.358527 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()`).
## 2024-04-30 23:57:15.622209 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()`).
## 2024-04-30 23:57:15.895596 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()`).
## 2024-04-30 23:57:16.159621 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()`).
## 2024-04-30 23:57:16.428623 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()`).
## 2024-04-30 23:57:16.710698 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()`).
## 2024-04-30 23:57:16.950134 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()`).
## 2024-04-30 23:57:17.193674 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()`).
## 2024-04-30 23:57:17.447708 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()`).
## 2024-04-30 23:57:17.706063 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()`).
## 2024-04-30 23:57:17.984294 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()`).
## 2024-04-30 23:57:18.222618 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()`).
## 2024-04-30 23:57:18.481335 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()`).
## 2024-04-30 23:57:18.727924 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()`).
## 2024-04-30 23:57:18.982051 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()`).
## 2024-04-30 23:57:19.225568 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()`).
## 2024-04-30 23:57:19.499338 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()`).
## 2024-04-30 23:57:19.770664 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()`).
## 2024-04-30 23:57:20.042028 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()`).
## 2024-04-30 23:57:23.472989 INFO::Plotting data for metadata number 6, diagnosis
## 2024-04-30 23:57:23.476058 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2024-04-30 23:57:23.716966 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-04-30 23:57:23.977616 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-04-30 23:57:24.233234 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-04-30 23:57:24.518233 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-04-30 23:57:24.762747 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2024-04-30 23:57:25.046366 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-04-30 23:57:25.315346 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-04-30 23:57:25.575794 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-04-30 23:57:25.814937 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-04-30 23:57:26.085329 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2024-04-30 23:57:26.450898 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-04-30 23:57:26.849241 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-04-30 23:57:27.233004 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-04-30 23:57:27.538804 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2024-04-30 23:57:27.803383 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2024-04-30 23:57:28.053108 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-04-30 23:57:28.310771 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-04-30 23:57:28.587178 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-04-30 23:57:28.884408 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-04-30 23:57:29.155459 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2024-04-30 23:57:29.408054 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-04-30 23:57:29.629627 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-04-30 23:57:29.861097 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-04-30 23:57:30.105628 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-04-30 23:57:30.314394 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2024-04-30 23:57:30.59604 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-04-30 23:57:30.879699 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-04-30 23:57:31.16507 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2024-04-30 23:57:31.45701 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2024-04-30 23:57:31.688034 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-04-30 23:57:31.958172 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2024-04-30 23:57:32.218685 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2024-04-30 23:57:32.491419 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-04-30 23:57:32.813355 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2024-04-30 23:57:33.092567 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2024-04-30 23:57:33.396781 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-04-30 23:57:33.683756 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2024-04-30 23:57:34.00217 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-04-30 23:57:34.27804 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-04-30 23:57:34.58754 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-04-30 23:57:34.874156 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-04-30 23:57:35.188106 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.siraeum
Session info from running the demo in R can be displayed with the following command.
sessionInfo()
## R version 4.4.0 beta (2024-04-14 r86421)
## Platform: x86_64-apple-darwin20
## Running under: macOS Monterey 12.7.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] Maaslin2_1.18.0
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.5 biglm_0.9-2.1 xfun_0.43
## [4] bslib_0.7.0 ggplot2_3.5.1 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_2.5.1
Run MaAsLin2 help to print a list of the options and the default settings.
$ Maaslin2.R –help Usage: ./R/Maaslin2.R options <data.tsv> <metadata.tsv>
Options: -h, –help Show this help message and exit
-a MIN_ABUNDANCE, --min_abundance=MIN_ABUNDANCE
The minimum abundance for each feature [ Default: 0 ]
-p MIN_PREVALENCE, --min_prevalence=MIN_PREVALENCE
The minimum percent of samples for which a feature
is detected at minimum abundance [ Default: 0.1 ]
-b MIN_VARIANCE, --min_variance=MIN_VARIANCE
Keep features with variance greater than [ Default: 0.0 ]
-s MAX_SIGNIFICANCE, --max_significance=MAX_SIGNIFICANCE
The q-value threshold for significance [ Default: 0.25 ]
-n NORMALIZATION, --normalization=NORMALIZATION
The normalization method to apply [ Default: TSS ]
[ Choices: TSS, CLR, CSS, NONE, TMM ]
-t TRANSFORM, --transform=TRANSFORM
The transform to apply [ Default: LOG ]
[ Choices: LOG, LOGIT, AST, NONE ]
-m ANALYSIS_METHOD, --analysis_method=ANALYSIS_METHOD
The analysis method to apply [ Default: LM ]
[ Choices: LM, CPLM, NEGBIN, ZINB ]
-r RANDOM_EFFECTS, --random_effects=RANDOM_EFFECTS
The random effects for the model, comma-delimited
for multiple effects [ Default: none ]
-f FIXED_EFFECTS, --fixed_effects=FIXED_EFFECTS
The fixed effects for the model, comma-delimited
for multiple effects [ Default: all ]
-c CORRECTION, --correction=CORRECTION
The correction method for computing the
q-value [ Default: BH ]
-z STANDARDIZE, --standardize=STANDARDIZE
Apply z-score so continuous metadata are
on the same scale [ Default: TRUE ]
-l PLOT_HEATMAP, --plot_heatmap=PLOT_HEATMAP
Generate a heatmap for the significant
associations [ Default: TRUE ]
-i HEATMAP_FIRST_N, --heatmap_first_n=HEATMAP_FIRST_N
In heatmap, plot top N features with significant
associations [ Default: TRUE ]
-o PLOT_SCATTER, --plot_scatter=PLOT_SCATTER
Generate scatter plots for the significant
associations [ Default: TRUE ]
-g MAX_PNGS, --max_pngs=MAX_PNGS
The maximum number of scatter plots for signficant associations
to save as png files [ Default: 10 ]
-O SAVE_SCATTER, --save_scatter=SAVE_SCATTER
Save all scatter plot ggplot objects
to an RData file [ Default: FALSE ]
-e CORES, --cores=CORES
The number of R processes to run in parallel
[ Default: 1 ]
-j SAVE_MODELS --save_models=SAVE_MODELS
Return the full model outputs and save to an RData file
[ Default: FALSE ]
-d REFERENCE, --reference=REFERENCE
The factor to use as a reference level for a categorical variable
provided as a string of 'variable,reference', semi-colon delimited for
multiple variables. Not required if metadata is passed as a factor or
for variables with less than two levels but can be set regardless.
[ Default: NA ]
Maaslin2.R: command not found
. How do I fix this?
Error in library(Maaslin2): there is no package called 'Maaslin2'
. How do I fix this?