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"
## 2024-11-08 17:54:53.786886 INFO::Writing function arguments to log file
## 2024-11-08 17:54:53.800099 INFO::Verifying options selected are valid
## 2024-11-08 17:54:53.813804 INFO::Determining format of input files
## 2024-11-08 17:54:53.814419 INFO::Input format is data samples as rows and metadata samples as rows
## 2024-11-08 17:54:53.81653 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2024-11-08 17:54:53.816985 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2024-11-08 17:54:53.817812 INFO::Filter data based on min abundance and min prevalence
## 2024-11-08 17:54:53.818064 INFO::Total samples in data: 1595
## 2024-11-08 17:54:53.818305 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2024-11-08 17:54:53.819984 INFO::Total filtered features: 0
## 2024-11-08 17:54:53.820273 INFO::Filtered feature names from abundance and prevalence filtering:
## 2024-11-08 17:54:53.823339 INFO::Total filtered features with variance filtering: 0
## 2024-11-08 17:54:53.823646 INFO::Filtered feature names from variance filtering:
## 2024-11-08 17:54:53.823884 INFO::Running selected normalization method: TSS
## 2024-11-08 17:54:54.243865 INFO::Bypass z-score application to metadata
## 2024-11-08 17:54:54.244316 INFO::Running selected transform method: LOG
## 2024-11-08 17:54:54.25081 INFO::Running selected analysis method: LM
## 2024-11-08 17:54:54.35847 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:54.479818 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2024-11-08 17:54:54.562845 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2024-11-08 17:54:54.693001 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:54.740196 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2024-11-08 17:54:54.79774 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:54.848439 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2024-11-08 17:54:54.893494 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2024-11-08 17:54:54.946432 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2024-11-08 17:54:54.998128 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2024-11-08 17:54:55.055091 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: -4.2e+01
## 2024-11-08 17:54:55.096685 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: -4.2e+01
## 2024-11-08 17:54:55.14625 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:55.19678 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:55.245337 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2024-11-08 17:54:55.292688 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:55.339079 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2024-11-08 17:54:55.393973 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2024-11-08 17:54:55.442136 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:55.488685 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:55.540783 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:55.588763 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:55.637149 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2024-11-08 17:54:55.687339 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2024-11-08 17:54:55.744754 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2024-11-08 17:54:55.799219 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2024-11-08 17:54:55.850699 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:55.906244 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2024-11-08 17:54:55.958822 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2024-11-08 17:54:56.010987 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:56.067155 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2024-11-08 17:54:56.120333 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2024-11-08 17:54:56.17113 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:56.226313 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:56.276494 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
## boundary (singular) fit: see help('isSingular')
## Feature Alistipes.onderdonkii : simpleWarning: Model failed to converge with 1 negative eigenvalue: -2.3e+00
## 2024-11-08 17:54:56.320744 WARNING::Fitting problem for feature 34 a warning was issued
## boundary (singular) fit: see help('isSingular')
## Warning: Model failed to converge with 1 negative eigenvalue: -2.3e+00
## 2024-11-08 17:54:56.377565 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:56.430156 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2024-11-08 17:54:56.482997 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2024-11-08 17:54:56.538668 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2024-11-08 17:54:56.593079 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:56.65372 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:56.705506 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:56.755783 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:56.813788 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2024-11-08 17:54:56.868683 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2024-11-08 17:54:56.920931 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:56.96974 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.018211 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2024-11-08 17:54:57.068403 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2024-11-08 17:54:57.11806 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.17174 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.217791 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.265687 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.314646 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.362451 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2024-11-08 17:54:57.41211 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2024-11-08 17:54:57.459303 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2024-11-08 17:54:57.614663 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.662722 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.714475 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.768549 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.817265 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2024-11-08 17:54:57.86221 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.910068 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:57.962729 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2024-11-08 17:54:58.014526 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2024-11-08 17:54:58.061901 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2024-11-08 17:54:58.114106 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:58.159277 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2024-11-08 17:54:58.205658 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2024-11-08 17:54:58.257935 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:58.305763 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2024-11-08 17:54:58.350938 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2024-11-08 17:54:58.401803 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:58.446212 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2024-11-08 17:54:58.493209 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:58.543557 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:58.587901 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2024-11-08 17:54:58.632758 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2024-11-08 17:54:58.683701 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2024-11-08 17:54:58.728123 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2024-11-08 17:54:58.775279 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2024-11-08 17:54:58.828528 INFO::Fitting model to feature number 82, Escherichia.coli
## 2024-11-08 17:54:58.874973 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2024-11-08 17:54:58.917763 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:58.965811 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2024-11-08 17:54:59.012389 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2024-11-08 17:54:59.060639 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2024-11-08 17:54:59.127034 INFO::Counting total values for each feature
## 2024-11-08 17:54:59.13831 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2024-11-08 17:54:59.181803 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2024-11-08 17:54:59.233543 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2024-11-08 17:54:59.304787 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2024-11-08 17:54:59.332095 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2024-11-08 17:54:59.346837 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2024-11-08 17:54:59.34952 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2024-11-08 17:54:59.352002 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
## 2024-11-08 17:54:59.353123 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2024-11-08 17:54:59.412445 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2024-11-08 17:54:59.415013 INFO::Plotting associations from most to least significant, grouped by metadata
## 2024-11-08 17:54:59.415389 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2024-11-08 17:54:59.41596 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2024-11-08 17:54:59.533009 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2024-11-08 17:54:59.615812 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2024-11-08 17:54:59.703741 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2024-11-08 17:54:59.780542 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2024-11-08 17:54:59.857406 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2024-11-08 17:54:59.936999 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2024-11-08 17:55:00.013276 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2024-11-08 17:55:00.092826 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2024-11-08 17:55:00.169352 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2024-11-08 17:55:00.250688 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2024-11-08 17:55:00.327496 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2024-11-08 17:55:00.407564 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2024-11-08 17:55:00.482368 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2024-11-08 17:55:00.561775 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2024-11-08 17:55:00.637799 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2024-11-08 17:55:00.718052 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2024-11-08 17:55:00.7953 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2024-11-08 17:55:00.873867 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2024-11-08 17:55:01.083973 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-11-08 17:55:01.161362 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2024-11-08 17:55:01.246184 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2024-11-08 17:55:01.32566 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2024-11-08 17:55:01.396783 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2024-11-08 17:55:01.475467 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2024-11-08 17:55:01.550746 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2024-11-08 17:55:01.630337 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2024-11-08 17:55:01.714207 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2024-11-08 17:55:01.802779 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2024-11-08 17:55:01.878755 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2024-11-08 17:55:01.955153 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2024-11-08 17:55:02.03303 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2024-11-08 17:55:02.115423 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2024-11-08 17:55:02.186207 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2024-11-08 17:55:02.266058 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2024-11-08 17:55:02.342101 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2024-11-08 17:55:02.4196 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2024-11-08 17:55:02.495403 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2024-11-08 17:55:02.575093 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2024-11-08 17:55:02.654537 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2024-11-08 17:55:02.737715 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2024-11-08 17:55:02.820683 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2024-11-08 17:55:02.908158 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2024-11-08 17:55:02.985138 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2024-11-08 17:55:03.074032 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2024-11-08 17:55:03.157444 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2024-11-08 17:55:03.240336 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2024-11-08 17:55:03.316535 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2024-11-08 17:55:03.392635 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2024-11-08 17:55:03.471379 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2024-11-08 17:55:03.553139 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2024-11-08 17:55:03.632392 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2024-11-08 17:55:03.716817 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2024-11-08 17:55:03.794974 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2024-11-08 17:55:03.878512 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2024-11-08 17:55:03.968485 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2024-11-08 17:55:04.056507 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2024-11-08 17:55:04.135696 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2024-11-08 17:55:04.219031 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2024-11-08 17:55:04.300459 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2024-11-08 17:55:04.385972 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2024-11-08 17:55:04.470981 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2024-11-08 17:55:04.556662 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-11-08 17:55:05.40698 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2024-11-08 17:55:05.407689 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2024-11-08 17:55:05.501726 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2024-11-08 17:55:05.582057 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2024-11-08 17:55:05.668158 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2024-11-08 17:55:05.751804 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2024-11-08 17:55:05.829457 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2024-11-08 17:55:05.913442 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2024-11-08 17:55:05.987764 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2024-11-08 17:55:06.074048 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2024-11-08 17:55:06.158402 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2024-11-08 17:55:06.247078 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2024-11-08 17:55:06.3334 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2024-11-08 17:55:06.425619 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-11-08 17:55:06.509133 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2024-11-08 17:55:06.600435 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2024-11-08 17:55:06.685097 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2024-11-08 17:55:06.774307 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2024-11-08 17:55:06.856298 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2024-11-08 17:55:06.944317 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2024-11-08 17:55:07.02476 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2024-11-08 17:55:07.114538 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2024-11-08 17:55:07.199245 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2024-11-08 17:55:07.292036 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2024-11-08 17:55:07.376161 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2024-11-08 17:55:07.466323 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2024-11-08 17:55:07.548675 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2024-11-08 17:55:07.640028 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2024-11-08 17:55:07.718404 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2024-11-08 17:55:07.80289 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2024-11-08 17:55:07.879133 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2024-11-08 17:55:07.960771 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2024-11-08 17:55:08.032749 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2024-11-08 17:55:08.119262 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2024-11-08 17:55:08.201154 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2024-11-08 17:55:08.288524 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2024-11-08 17:55:08.371492 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2024-11-08 17:55:08.453448 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2024-11-08 17:55:08.543876 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2024-11-08 17:55:08.626137 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2024-11-08 17:55:08.716454 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2024-11-08 17:55:08.801355 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2024-11-08 17:55:08.89407 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2024-11-08 17:55:08.976798 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2024-11-08 17:55:09.09275 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2024-11-08 17:55:09.939925 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2024-11-08 17:55:09.940629 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2024-11-08 17:55:10.001615 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2024-11-08 17:55:10.090134 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2024-11-08 17:55:10.169855 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2024-11-08 17:55:10.253084 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2024-11-08 17:55:10.331771 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-11-08 17:55:10.420236 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2024-11-08 17:55:10.496721 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2024-11-08 17:55:10.586471 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2024-11-08 17:55:10.664626 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2024-11-08 17:55:10.750984 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2024-11-08 17:55:10.831377 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2024-11-08 17:55:10.921341 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2024-11-08 17:55:10.999202 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2024-11-08 17:55:11.091353 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2024-11-08 17:55:11.171697 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2024-11-08 17:55:11.254032 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2024-11-08 17:55:11.330071 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2024-11-08 17:55:11.419648 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2024-11-08 17:55:11.494623 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2024-11-08 17:55:11.580505 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2024-11-08 17:55:11.658604 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2024-11-08 17:55:11.748528 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2024-11-08 17:55:11.82997 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2024-11-08 17:55:11.917317 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2024-11-08 17:55:12.002796 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2024-11-08 17:55:12.082421 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2024-11-08 17:55:12.165409 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2024-11-08 17:55:12.244213 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2024-11-08 17:55:13.138722 INFO::Plotting data for metadata number 4, antibiotics
## 2024-11-08 17:55:13.13961 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2024-11-08 17:55:13.214515 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2024-11-08 17:55:13.302468 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2024-11-08 17:55:13.400992 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2024-11-08 17:55:13.4869 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2024-11-08 17:55:13.567293 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2024-11-08 17:55:13.659887 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2024-11-08 17:55:13.741508 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2024-11-08 17:55:13.828783 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2024-11-08 17:55:13.906884 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2024-11-08 17:55:14.000371 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2024-11-08 17:55:14.079152 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2024-11-08 17:55:14.167841 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2024-11-08 17:55:14.251895 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2024-11-08 17:55:14.343815 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2024-11-08 17:55:14.424628 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-11-08 17:55:14.518195 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2024-11-08 17:55:14.600266 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2024-11-08 17:55:14.688752 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2024-11-08 17:55:14.766332 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2024-11-08 17:55:14.853331 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2024-11-08 17:55:14.929816 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2024-11-08 17:55:15.011571 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2024-11-08 17:55:15.091603 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2024-11-08 17:55:15.184253 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2024-11-08 17:55:15.268507 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2024-11-08 17:55:15.35741 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2024-11-08 17:55:15.44399 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2024-11-08 17:55:15.530855 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2024-11-08 17:55:15.615926 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2024-11-08 17:55:15.704944 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2024-11-08 17:55:15.786004 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2024-11-08 17:55:15.874939 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2024-11-08 17:55:15.956618 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2024-11-08 17:55:16.047393 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2024-11-08 17:55:16.126678 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2024-11-08 17:55:16.241375 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-11-08 17:55:16.324173 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2024-11-08 17:55:16.414673 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2024-11-08 17:55:16.492524 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2024-11-08 17:55:17.318541 INFO::Plotting data for metadata number 5, age
## 2024-11-08 17:55:17.319288 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()`).
## 2024-11-08 17:55:17.402466 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()`).
## 2024-11-08 17:55:17.51788 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()`).
## 2024-11-08 17:55:17.601489 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()`).
## 2024-11-08 17:55:17.683358 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()`).
## 2024-11-08 17:55:17.769609 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()`).
## 2024-11-08 17:55:17.848339 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()`).
## 2024-11-08 17:55:17.947333 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()`).
## 2024-11-08 17:55:18.036315 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()`).
## 2024-11-08 17:55:18.116644 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()`).
## 2024-11-08 17:55:18.20909 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()`).
## 2024-11-08 17:55:18.285877 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()`).
## 2024-11-08 17:55:18.378333 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()`).
## 2024-11-08 17:55:18.47423 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()`).
## 2024-11-08 17:55:18.550292 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()`).
## 2024-11-08 17:55:18.6374 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()`).
## 2024-11-08 17:55:18.721156 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()`).
## 2024-11-08 17:55:18.804628 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()`).
## 2024-11-08 17:55:18.898164 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()`).
## 2024-11-08 17:55:18.978811 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()`).
## 2024-11-08 17:55:19.064628 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()`).
## 2024-11-08 17:55:19.150145 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()`).
## 2024-11-08 17:55:20.148322 INFO::Plotting data for metadata number 6, diagnosis
## 2024-11-08 17:55:20.149063 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2024-11-08 17:55:20.217047 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-11-08 17:55:20.296305 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-11-08 17:55:20.380738 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-11-08 17:55:20.463502 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-11-08 17:55:20.547941 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2024-11-08 17:55:20.628016 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-11-08 17:55:20.711258 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-11-08 17:55:20.791054 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-11-08 17:55:20.875127 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-11-08 17:55:20.957669 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2024-11-08 17:55:21.043789 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-11-08 17:55:21.126508 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-11-08 17:55:21.210754 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-11-08 17:55:21.291338 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2024-11-08 17:55:21.37451 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2024-11-08 17:55:21.451781 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-11-08 17:55:21.53774 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-11-08 17:55:21.619524 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-11-08 17:55:21.704846 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-11-08 17:55:21.782867 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2024-11-08 17:55:21.867552 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-11-08 17:55:21.948676 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-11-08 17:55:22.034314 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-11-08 17:55:22.112244 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-11-08 17:55:22.193322 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2024-11-08 17:55:22.275188 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-11-08 17:55:22.359974 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-11-08 17:55:22.455674 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2024-11-08 17:55:22.541303 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2024-11-08 17:55:22.62974 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-11-08 17:55:22.710281 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2024-11-08 17:55:22.795055 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2024-11-08 17:55:22.879049 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-11-08 17:55:22.988685 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2024-11-08 17:55:23.073394 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2024-11-08 17:55:23.164689 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-11-08 17:55:23.238523 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2024-11-08 17:55:23.320554 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-11-08 17:55:23.392303 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-11-08 17:55:23.478702 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-11-08 17:55:23.562473 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-11-08 17:55:23.652231 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 4.4.1 (2024-06-14)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.6.7
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] Maaslin2_1.20.0
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.6 biglm_0.9-3 xfun_0.49
## [4] bslib_0.8.0 ggplot2_3.5.1 lattice_0.22-6
## [7] numDeriv_2016.8-1.1 vctrs_0.6.5 tools_4.4.1
## [10] generics_0.1.3 parallel_4.4.1 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_1.7-1 data.table_1.16.2
## [22] RColorBrewer_1.1-3 lifecycle_1.0.4 farver_2.1.2
## [25] compiler_4.4.1 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_2.3.10 pillar_1.9.0
## [34] nloptr_2.1.1 crayon_1.5.3 jquerylib_0.1.4
## [37] MASS_7.3-61 cachem_1.1.0 vegan_2.6-8
## [40] boot_1.3-31 nlme_3.1-166 robustbase_0.99-4-1
## [43] tidyselect_1.2.1 digest_0.6.37 mvtnorm_1.3-2
## [46] dplyr_1.1.4 labeling_0.4.3 splines_4.4.1
## [49] pcaPP_2.0-5 fastmap_1.2.0 grid_4.4.1
## [52] colorspace_2.1-1 cli_3.6.3 magrittr_2.0.3
## [55] utf8_1.2.4 withr_3.0.2 scales_1.3.0
## [58] rmarkdown_2.29 lme4_1.1-35.5 pbapply_1.7-2
## [61] evaluate_1.0.1 knitr_1.49 mgcv_1.9-1
## [64] rlang_1.1.4 Rcpp_1.0.13-1 glue_1.8.0
## [67] optparse_1.7.5 DBI_1.2.3 minqa_1.2.8
## [70] jsonlite_1.8.9 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?