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 20:47:52.174559 INFO::Writing function arguments to log file
## 2024-04-30 20:47:52.201892 INFO::Verifying options selected are valid
## 2024-04-30 20:47:52.252434 INFO::Determining format of input files
## 2024-04-30 20:47:52.254039 INFO::Input format is data samples as rows and metadata samples as rows
## 2024-04-30 20:47:52.259698 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2024-04-30 20:47:52.260916 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2024-04-30 20:47:52.263221 INFO::Filter data based on min abundance and min prevalence
## 2024-04-30 20:47:52.263925 INFO::Total samples in data: 1595
## 2024-04-30 20:47:52.264631 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2024-04-30 20:47:52.269719 INFO::Total filtered features: 0
## 2024-04-30 20:47:52.270757 INFO::Filtered feature names from abundance and prevalence filtering:
## 2024-04-30 20:47:52.280547 INFO::Total filtered features with variance filtering: 0
## 2024-04-30 20:47:52.281619 INFO::Filtered feature names from variance filtering:
## 2024-04-30 20:47:52.282319 INFO::Running selected normalization method: TSS
## 2024-04-30 20:47:53.573017 INFO::Bypass z-score application to metadata
## 2024-04-30 20:47:53.575141 INFO::Running selected transform method: LOG
## 2024-04-30 20:47:53.596046 INFO::Running selected analysis method: LM
## 2024-04-30 20:47:53.93236 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:54.319359 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2024-04-30 20:47:54.514358 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2024-04-30 20:47:54.783034 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:55.230076 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2024-04-30 20:47:55.411906 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:55.582848 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2024-04-30 20:47:55.75264 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2024-04-30 20:47:55.942401 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2024-04-30 20:47:56.10777 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2024-04-30 20:47:56.283431 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
## 2024-04-30 20:47:56.421658 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
## 2024-04-30 20:47:56.600435 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:56.767067 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:56.942765 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2024-04-30 20:47:57.12592 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:57.288495 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2024-04-30 20:47:57.465435 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2024-04-30 20:47:57.632898 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:57.801759 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:57.965579 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:58.13359 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:58.311208 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2024-04-30 20:47:58.47225 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2024-04-30 20:47:58.641186 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2024-04-30 20:47:58.825775 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2024-04-30 20:47:58.990499 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:59.154638 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2024-04-30 20:47:59.326464 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2024-04-30 20:47:59.50494 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:47:59.672525 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2024-04-30 20:47:59.850278 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2024-04-30 20:48:00.028891 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:00.197869 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:00.361894 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
## 2024-04-30 20:48:00.513786 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
## 2024-04-30 20:48:00.688066 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:00.862644 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2024-04-30 20:48:01.050156 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2024-04-30 20:48:01.220875 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2024-04-30 20:48:01.403859 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:01.581381 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:01.741689 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:01.918379 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:02.085453 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2024-04-30 20:48:02.277099 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2024-04-30 20:48:02.439262 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:02.60134 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:02.78089 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2024-04-30 20:48:02.949437 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2024-04-30 20:48:03.138534 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:03.323449 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:03.49305 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:03.661032 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:03.829002 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:03.996164 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2024-04-30 20:48:04.169413 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2024-04-30 20:48:04.331796 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2024-04-30 20:48:04.510295 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:04.682195 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:04.867065 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:05.04957 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:05.226635 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2024-04-30 20:48:05.398084 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:05.604193 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:05.776753 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2024-04-30 20:48:05.967182 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2024-04-30 20:48:06.171607 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2024-04-30 20:48:06.345248 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:06.506081 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2024-04-30 20:48:06.67538 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2024-04-30 20:48:06.867824 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:07.038489 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2024-04-30 20:48:07.1987 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2024-04-30 20:48:07.384818 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:07.551125 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2024-04-30 20:48:07.71879 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:07.89849 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:08.060935 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2024-04-30 20:48:08.22338 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2024-04-30 20:48:08.406976 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2024-04-30 20:48:08.572105 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2024-04-30 20:48:08.744574 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2024-04-30 20:48:08.941511 INFO::Fitting model to feature number 82, Escherichia.coli
## 2024-04-30 20:48:09.117451 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2024-04-30 20:48:09.28137 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:09.462512 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2024-04-30 20:48:09.6342 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2024-04-30 20:48:09.818826 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2024-04-30 20:48:10.031636 INFO::Counting total values for each feature
## 2024-04-30 20:48:10.070004 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2024-04-30 20:48:10.230025 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2024-04-30 20:48:10.404556 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2024-04-30 20:48:10.661141 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2024-04-30 20:48:10.750619 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2024-04-30 20:48:10.799841 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2024-04-30 20:48:10.809071 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2024-04-30 20:48:10.817979 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 20:48:10.822277 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2024-04-30 20:48:11.000413 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2024-04-30 20:48:11.008823 INFO::Plotting associations from most to least significant, grouped by metadata
## 2024-04-30 20:48:11.010208 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2024-04-30 20:48:11.012387 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2024-04-30 20:48:11.405929 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2024-04-30 20:48:11.740584 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2024-04-30 20:48:12.022686 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2024-04-30 20:48:12.30578 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2024-04-30 20:48:12.581604 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2024-04-30 20:48:12.869785 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2024-04-30 20:48:13.156581 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2024-04-30 20:48:13.458714 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2024-04-30 20:48:13.741809 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2024-04-30 20:48:14.045619 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2024-04-30 20:48:14.320622 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2024-04-30 20:48:14.97186 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2024-04-30 20:48:15.241864 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2024-04-30 20:48:15.527004 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2024-04-30 20:48:15.805304 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2024-04-30 20:48:16.08139 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2024-04-30 20:48:16.376129 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2024-04-30 20:48:16.654286 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2024-04-30 20:48:16.923863 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-04-30 20:48:17.210361 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2024-04-30 20:48:17.48534 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2024-04-30 20:48:17.769488 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2024-04-30 20:48:18.035229 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2024-04-30 20:48:18.363318 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2024-04-30 20:48:18.650226 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2024-04-30 20:48:18.945309 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2024-04-30 20:48:19.216149 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2024-04-30 20:48:19.507679 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2024-04-30 20:48:19.794638 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2024-04-30 20:48:20.073925 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2024-04-30 20:48:20.343061 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2024-04-30 20:48:20.616051 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2024-04-30 20:48:20.879765 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2024-04-30 20:48:21.168946 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2024-04-30 20:48:21.4543 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2024-04-30 20:48:21.73835 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2024-04-30 20:48:22.00893 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2024-04-30 20:48:22.287863 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2024-04-30 20:48:22.556911 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2024-04-30 20:48:22.838868 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2024-04-30 20:48:23.121102 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2024-04-30 20:48:23.410473 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2024-04-30 20:48:23.676156 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2024-04-30 20:48:23.94625 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2024-04-30 20:48:24.204592 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2024-04-30 20:48:24.482869 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2024-04-30 20:48:24.756696 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2024-04-30 20:48:25.031069 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2024-04-30 20:48:25.336176 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2024-04-30 20:48:25.613144 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2024-04-30 20:48:25.894429 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2024-04-30 20:48:26.1788 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2024-04-30 20:48:26.463606 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2024-04-30 20:48:26.726004 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2024-04-30 20:48:27.008057 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2024-04-30 20:48:27.272627 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2024-04-30 20:48:27.545378 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2024-04-30 20:48:27.806686 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2024-04-30 20:48:28.088157 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2024-04-30 20:48:28.367503 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2024-04-30 20:48:28.655568 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2024-04-30 20:48:28.94321 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-04-30 20:48:31.827893 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2024-04-30 20:48:31.83063 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2024-04-30 20:48:32.04602 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2024-04-30 20:48:32.354802 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2024-04-30 20:48:32.643801 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2024-04-30 20:48:32.944255 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2024-04-30 20:48:33.227854 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2024-04-30 20:48:33.538237 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2024-04-30 20:48:33.807757 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2024-04-30 20:48:34.110892 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2024-04-30 20:48:34.393154 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2024-04-30 20:48:34.686388 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2024-04-30 20:48:34.966045 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2024-04-30 20:48:35.266462 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-04-30 20:48:35.543087 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2024-04-30 20:48:35.849206 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2024-04-30 20:48:36.124492 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2024-04-30 20:48:36.428423 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2024-04-30 20:48:36.712786 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2024-04-30 20:48:37.020707 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2024-04-30 20:48:37.28574 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2024-04-30 20:48:37.587563 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2024-04-30 20:48:37.860142 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2024-04-30 20:48:38.161395 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2024-04-30 20:48:38.448027 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2024-04-30 20:48:38.745153 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2024-04-30 20:48:39.048408 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2024-04-30 20:48:39.330697 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2024-04-30 20:48:39.614885 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2024-04-30 20:48:39.875103 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2024-04-30 20:48:40.192338 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2024-04-30 20:48:40.471445 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2024-04-30 20:48:40.749383 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2024-04-30 20:48:41.031997 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2024-04-30 20:48:41.41787 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2024-04-30 20:48:41.720302 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2024-04-30 20:48:42.013199 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2024-04-30 20:48:42.29154 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2024-04-30 20:48:42.595593 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2024-04-30 20:48:42.868238 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2024-04-30 20:48:43.171619 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2024-04-30 20:48:43.448821 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2024-04-30 20:48:43.759153 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2024-04-30 20:48:44.031932 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2024-04-30 20:48:44.34793 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2024-04-30 20:48:47.188762 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2024-04-30 20:48:47.191209 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2024-04-30 20:48:47.432336 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2024-04-30 20:48:47.723062 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2024-04-30 20:48:48.036508 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2024-04-30 20:48:48.303158 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2024-04-30 20:48:48.60653 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-04-30 20:48:48.888265 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2024-04-30 20:48:49.189201 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2024-04-30 20:48:49.469099 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2024-04-30 20:48:49.760963 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2024-04-30 20:48:50.030216 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2024-04-30 20:48:50.32202 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2024-04-30 20:48:50.619013 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2024-04-30 20:48:50.916722 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2024-04-30 20:48:51.226172 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2024-04-30 20:48:51.505928 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2024-04-30 20:48:51.787638 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2024-04-30 20:48:52.060343 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2024-04-30 20:48:52.370864 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2024-04-30 20:48:52.638881 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2024-04-30 20:48:53.010048 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2024-04-30 20:48:53.295819 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2024-04-30 20:48:53.616384 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2024-04-30 20:48:53.893062 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2024-04-30 20:48:54.193031 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2024-04-30 20:48:54.464708 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2024-04-30 20:48:54.768892 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2024-04-30 20:48:55.039567 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2024-04-30 20:48:55.36331 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2024-04-30 20:48:58.288825 INFO::Plotting data for metadata number 4, antibiotics
## 2024-04-30 20:48:58.291292 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2024-04-30 20:48:58.532809 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2024-04-30 20:48:58.814139 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2024-04-30 20:48:59.126975 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2024-04-30 20:48:59.41192 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2024-04-30 20:48:59.714562 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2024-04-30 20:48:59.986286 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2024-04-30 20:49:00.291364 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2024-04-30 20:49:00.573985 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2024-04-30 20:49:00.859089 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2024-04-30 20:49:01.126633 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2024-04-30 20:49:01.412701 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2024-04-30 20:49:01.653529 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2024-04-30 20:49:01.959048 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2024-04-30 20:49:02.221077 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2024-04-30 20:49:02.506547 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-04-30 20:49:02.757054 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2024-04-30 20:49:03.052675 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2024-04-30 20:49:03.311069 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2024-04-30 20:49:03.597063 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2024-04-30 20:49:03.858639 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2024-04-30 20:49:04.15268 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2024-04-30 20:49:04.413377 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2024-04-30 20:49:04.830253 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2024-04-30 20:49:05.105399 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2024-04-30 20:49:05.421571 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2024-04-30 20:49:05.681092 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2024-04-30 20:49:05.984345 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2024-04-30 20:49:06.23468 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2024-04-30 20:49:06.532123 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2024-04-30 20:49:06.783903 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2024-04-30 20:49:07.071083 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2024-04-30 20:49:07.322494 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2024-04-30 20:49:07.609679 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2024-04-30 20:49:07.872715 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2024-04-30 20:49:08.169931 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2024-04-30 20:49:08.427534 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-04-30 20:49:08.732686 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2024-04-30 20:49:08.995002 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2024-04-30 20:49:09.293596 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2024-04-30 20:49:12.123545 INFO::Plotting data for metadata number 5, age
## 2024-04-30 20:49:12.126155 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 20:49:12.413499 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 20:49:12.804466 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 20:49:13.08915 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 20:49:13.424627 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 20:49:13.685042 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 20:49:13.992232 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 20:49:14.315183 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 20:49:14.590173 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 20:49:14.894497 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 20:49:15.18702 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 20:49:15.471296 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 20:49:16.199462 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 20:49:16.45715 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 20:49:16.709232 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 20:49:16.955594 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 20:49:17.206588 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 20:49:17.457647 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 20:49:17.697115 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 20:49:17.953665 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 20:49:18.212191 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 20:49:18.462199 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 20:49:21.227519 INFO::Plotting data for metadata number 6, diagnosis
## 2024-04-30 20:49:21.230235 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2024-04-30 20:49:21.445115 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-04-30 20:49:21.721091 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-04-30 20:49:21.984483 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-04-30 20:49:22.269546 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-04-30 20:49:22.532949 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2024-04-30 20:49:22.806121 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-04-30 20:49:23.06946 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-04-30 20:49:23.349276 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-04-30 20:49:23.626166 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-04-30 20:49:23.908006 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2024-04-30 20:49:24.192112 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-04-30 20:49:24.454472 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-04-30 20:49:24.714115 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-04-30 20:49:24.968699 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2024-04-30 20:49:25.243446 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2024-04-30 20:49:25.503574 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-04-30 20:49:25.784328 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-04-30 20:49:26.151748 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-04-30 20:49:26.439192 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-04-30 20:49:26.736844 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2024-04-30 20:49:27.013885 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-04-30 20:49:27.293194 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-04-30 20:49:27.572083 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-04-30 20:49:27.866096 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-04-30 20:49:28.13352 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2024-04-30 20:49:28.421624 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-04-30 20:49:28.696098 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-04-30 20:49:28.993081 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2024-04-30 20:49:29.272855 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2024-04-30 20:49:29.569546 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-04-30 20:49:29.860064 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2024-04-30 20:49:30.138434 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2024-04-30 20:49:30.413883 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-04-30 20:49:30.712752 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2024-04-30 20:49:30.993702 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2024-04-30 20:49:31.28838 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-04-30 20:49:31.585968 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2024-04-30 20:49:31.879272 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-04-30 20:49:32.153913 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-04-30 20:49:32.307337 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-04-30 20:49:32.496674 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-04-30 20:49:32.673197 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 Patched (2024-04-24 r86482)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.6.6
##
## 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_1.17.0
##
## 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?