MaAsLin2 is the next generation of MaAsLin (Microbiome Multivariable Association with Linear Models).
MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta-omics features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, along with a variety of filtering, normalization, and transform methods.
If you use the MaAsLin2 software, please cite our manuscript:
Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C (2021). Multivariable Association Discovery in Population-scale Meta-omics Studies. PLoS Computational Biology, 17(11):e1009442.
Check out the MaAsLin 2 tutorial for an overview of analysis options.
If you have questions, please direct it to :
MaAsLin2 Forum
Google Groups (Read only)
MaAsLin2 finds associations between microbiome multi-omics features and complex metadata in population-scale epidemiological studies. The software includes multiple analysis methods (with support for multiple covariates and repeated measures), filtering, normalization, and transform options to customize analysis for your specific study.
MaAsLin2 is an R package that can be run on the command line or as an R function.
MaAsLin2 can be run from the command line or as an R function. If only running from the command line, you do not need to install the MaAsLin2 package but you will need to install the MaAsLin2 dependencies.
$ tar xzvf maaslin2.tar.gz$ R -q -e "install.packages(c('lmerTest','pbapply','car','dplyr','vegan','chemometrics','ggplot2','pheatmap','hash','logging','data.table','glmmTMB','MASS','cplm','pscl'), repos='http://cran.r-project.org')"$ R CMD INSTALL maaslin2Install Bioconductor and then install Maaslin2
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Maaslin2")MaAsLin2 can be run from the command line or as an R function. Both methods require the same arguments, have the same options, and use the same default settings.
MaAsLin2 requires two input files.
The data file can contain samples not included in the metadata file (along with the reverse case). For both cases, those samples not included in both files will be removed from the analysis. Also the samples do not need to be in the same order in the two files.
NOTE: If running MaAsLin2 as a function, the data and metadata inputs can be of type data.frame instead of a path to a file.
MaAsLin2 generates two types of output files: data and visualization.
all_results.tsv
N column is the total number of data points.N.not.zero column is the total of non-zero data points.p.adjust with the correction method.significant_results.tsv
models.rds
residuals.rds
fitted.rds
ranef.rds
maaslin2.log
heatmap.pdf
[a-z/0-9]+.pdf
Example input files can be found in the inst/extdata folder of the MaAsLin2 source. The files provided were generated from the HMP2 data which can be downloaded from https://ibdmdb.org/ .
HMP2_taxonomy.tsv: is a tab-demilited file with species as columns and samples as rows. It is a subset of the taxonomy file so it just includes the species abundances for all samples.
HMP2_metadata.tsv: is a tab-delimited file with samples as rows and metadata as columns. It is a subset of the metadata file so that it just includes some of the fields.
$ Maaslin2.R --fixed_effects="diagnosis,dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age" --random_effects="site,subject" --standardize=FALSE inst/extdata/HMP2_taxonomy.tsv inst/extdata/HMP2_metadata.tsv demo_output
HMP2_taxonomy.tsv is the path to your data (or features) fileHMP2_metadata.tsv is the path to your metadata filedemo_output is the path to the folder to write the outputlibrary(Maaslin2)
input_data <- system.file(
'extdata','HMP2_taxonomy.tsv', package="Maaslin2")
input_metadata <-system.file(
'extdata','HMP2_metadata.tsv', package="Maaslin2")
fit_data <- Maaslin2(
input_data, input_metadata, 'demo_output',
fixed_effects = c('diagnosis', 'dysbiosisnonIBD','dysbiosisUC','dysbiosisCD', 'antibiotics', 'age'),
random_effects = c('site', 'subject'),
reference = "diagnosis,nonIBD",
standardize = FALSE)## [1] "Creating output folder"
## [1] "Creating output feature tables folder"
## [1] "Creating output fits folder"
## [1] "Creating output figures folder"
## 2023-10-24 17:44:41.011281 INFO::Writing function arguments to log file
## 2023-10-24 17:44:41.034445 INFO::Verifying options selected are valid
## 2023-10-24 17:44:41.068672 INFO::Determining format of input files
## 2023-10-24 17:44:41.069822 INFO::Input format is data samples as rows and metadata samples as rows
## 2023-10-24 17:44:41.074811 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2023-10-24 17:44:41.075849 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2023-10-24 17:44:41.078061 INFO::Filter data based on min abundance and min prevalence
## 2023-10-24 17:44:41.07872 INFO::Total samples in data: 1595
## 2023-10-24 17:44:41.079331 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2023-10-24 17:44:41.091234 INFO::Total filtered features: 0
## 2023-10-24 17:44:41.092082 INFO::Filtered feature names from abundance and prevalence filtering:
## 2023-10-24 17:44:41.09888 INFO::Total filtered features with variance filtering: 0
## 2023-10-24 17:44:41.099596 INFO::Filtered feature names from variance filtering:
## 2023-10-24 17:44:41.10023 INFO::Running selected normalization method: TSS
## 2023-10-24 17:44:42.209831 INFO::Bypass z-score application to metadata
## 2023-10-24 17:44:42.210753 INFO::Running selected transform method: LOG
## 2023-10-24 17:44:42.228153 INFO::Running selected analysis method: LM
## 2023-10-24 17:44:42.757542 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:43.069015 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2023-10-24 17:44:43.233487 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2023-10-24 17:44:43.385234 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:43.51916 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2023-10-24 17:44:43.667278 INFO::Fitting model to feature number 6, Bacteroides.caccae## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:43.808948 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2023-10-24 17:44:43.94207 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2023-10-24 17:44:44.085616 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2023-10-24 17:44:44.221177 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2023-10-24 17:44:44.378144 INFO::Fitting model to feature number 11, Bacteroides.finegoldii## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:44.515978 INFO::Fitting model to feature number 12, Bacteroides.fragilis## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:44.649218 INFO::Fitting model to feature number 13, Bacteroides.intestinalis## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:44.792101 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2023-10-24 17:44:44.925852 INFO::Fitting model to feature number 15, Bacteroides.ovatus## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:45.055833 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2023-10-24 17:44:45.192841 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2023-10-24 17:44:45.337684 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:45.47471 INFO::Fitting model to feature number 19, Bacteroides.uniformis## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:45.615048 INFO::Fitting model to feature number 20, Bacteroides.vulgatus## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:45.758259 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:45.902524 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2023-10-24 17:44:46.102466 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2023-10-24 17:44:46.333452 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2023-10-24 17:44:46.520978 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2023-10-24 17:44:46.672982 INFO::Fitting model to feature number 26, Parabacteroides.distasonis## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:47.145335 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2023-10-24 17:44:47.29201 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2023-10-24 17:44:47.440143 INFO::Fitting model to feature number 29, Parabacteroides.unclassified## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:47.606673 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2023-10-24 17:44:47.769508 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2023-10-24 17:44:47.91563 INFO::Fitting model to feature number 32, Prevotella.copri## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:48.071066 INFO::Fitting model to feature number 33, Alistipes.finegoldii## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:48.222873 INFO::Fitting model to feature number 34, Alistipes.onderdonkii## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:48.362805 INFO::Fitting model to feature number 35, Alistipes.putredinis## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:48.500791 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2023-10-24 17:44:48.656806 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2023-10-24 17:44:48.811683 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2023-10-24 17:44:48.984056 INFO::Fitting model to feature number 39, Clostridium.bolteae## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:49.175913 INFO::Fitting model to feature number 40, Clostridium.citroniae## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:49.313212 INFO::Fitting model to feature number 41, Clostridium.clostridioforme## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:49.447044 INFO::Fitting model to feature number 42, Clostridium.hathewayi## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:49.598212 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2023-10-24 17:44:49.746774 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2023-10-24 17:44:49.880623 INFO::Fitting model to feature number 45, Clostridium.symbiosum## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:50.02052 INFO::Fitting model to feature number 46, Flavonifractor.plautii## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:50.157965 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2023-10-24 17:44:50.298905 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2023-10-24 17:44:50.460993 INFO::Fitting model to feature number 49, Eubacterium.rectale## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:50.609555 INFO::Fitting model to feature number 50, Eubacterium.siraeum## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:50.74849 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:50.890951 INFO::Fitting model to feature number 52, Eubacterium.ventriosum## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:51.018132 INFO::Fitting model to feature number 53, Ruminococcus.gnavus## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:51.155966 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2023-10-24 17:44:51.303506 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2023-10-24 17:44:51.437767 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2023-10-24 17:44:51.582726 INFO::Fitting model to feature number 57, Dorea.longicatena## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:51.722383 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:51.862806 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:52.004289 INFO::Fitting model to feature number 60, Roseburia.hominis## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:52.142279 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2023-10-24 17:44:52.285374 INFO::Fitting model to feature number 62, Roseburia.inulinivorans## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:52.432156 INFO::Fitting model to feature number 63, Roseburia.unclassified## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:52.591457 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2023-10-24 17:44:52.735017 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2023-10-24 17:44:52.876414 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2023-10-24 17:44:53.013921 INFO::Fitting model to feature number 67, Ruminococcus.bromii## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:53.147995 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2023-10-24 17:44:53.277578 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2023-10-24 17:44:53.425639 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:53.563074 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2023-10-24 17:44:53.705981 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2023-10-24 17:44:53.842474 INFO::Fitting model to feature number 73, Dialister.invisus## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:53.977816 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2023-10-24 17:44:54.127614 INFO::Fitting model to feature number 75, Veillonella.dispar## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:54.261925 INFO::Fitting model to feature number 76, Veillonella.parvula## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:54.39258 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2023-10-24 17:44:54.529444 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2023-10-24 17:44:54.664613 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2023-10-24 17:44:54.802927 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2023-10-24 17:44:54.967761 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2023-10-24 17:44:55.117829 INFO::Fitting model to feature number 82, Escherichia.coli
## 2023-10-24 17:44:55.261224 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2023-10-24 17:44:55.399481 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:55.529468 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae## boundary (singular) fit: see help('isSingular')## 2023-10-24 17:44:55.664994 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2023-10-24 17:44:56.118544 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2023-10-24 17:44:56.304755 INFO::Counting total values for each feature
## 2023-10-24 17:44:56.340361 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2023-10-24 17:44:56.484721 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2023-10-24 17:44:56.634074 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2023-10-24 17:44:56.868073 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2023-10-24 17:44:56.930016 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2023-10-24 17:44:56.964873 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2023-10-24 17:44:56.970334 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2023-10-24 17:44:56.976756 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
## 2023-10-24 17:44:56.979732 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2023-10-24 17:44:57.207036 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2023-10-24 17:44:57.213591 INFO::Plotting associations from most to least significant, grouped by metadata
## 2023-10-24 17:44:57.214557 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2023-10-24 17:44:57.216146 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii## 2023-10-24 17:44:57.565697 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified## 2023-10-24 17:44:57.825143 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis## 2023-10-24 17:44:58.066739 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale## 2023-10-24 17:44:58.357526 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus## 2023-10-24 17:44:58.617296 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus## 2023-10-24 17:44:58.865844 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum## 2023-10-24 17:44:59.110052 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified## 2023-10-24 17:44:59.361034 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans## 2023-10-24 17:44:59.615569 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis## 2023-10-24 17:44:59.859553 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron## 2023-10-24 17:45:00.115715 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis## 2023-10-24 17:45:00.379692 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis## 2023-10-24 17:45:00.635076 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei## 2023-10-24 17:45:00.876679 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii## 2023-10-24 17:45:01.11948 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens## 2023-10-24 17:45:01.369218 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum## 2023-10-24 17:45:01.608164 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena## 2023-10-24 17:45:01.85331 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae## 2023-10-24 17:45:02.09592 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA## 2023-10-24 17:45:02.342162 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli## 2023-10-24 17:45:02.622881 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae## 2023-10-24 17:45:02.870835 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified## 2023-10-24 17:45:03.106959 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii## 2023-10-24 17:45:03.354284 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens## 2023-10-24 17:45:03.591412 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris## 2023-10-24 17:45:03.842288 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes## 2023-10-24 17:45:04.08482 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis## 2023-10-24 17:45:04.670054 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii## 2023-10-24 17:45:04.923273 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii## 2023-10-24 17:45:05.161884 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis## 2023-10-24 17:45:05.406422 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara## 2023-10-24 17:45:05.635548 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum## 2023-10-24 17:45:05.86776 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae## 2023-10-24 17:45:06.098581 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified## 2023-10-24 17:45:06.341379 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens## 2023-10-24 17:45:06.577921 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus## 2023-10-24 17:45:06.813843 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme## 2023-10-24 17:45:07.056669 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii## 2023-10-24 17:45:07.286274 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii## 2023-10-24 17:45:07.526088 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum## 2023-10-24 17:45:07.781662 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris## 2023-10-24 17:45:08.028828 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47## 2023-10-24 17:45:08.262586 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus## 2023-10-24 17:45:08.494666 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii## 2023-10-24 17:45:08.735177 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis## 2023-10-24 17:45:08.969666 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified## 2023-10-24 17:45:09.201615 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques## 2023-10-24 17:45:09.43356 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified## 2023-10-24 17:45:09.670281 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus## 2023-10-24 17:45:09.902374 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis## 2023-10-24 17:45:10.142475 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified## 2023-10-24 17:45:10.380103 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified## 2023-10-24 17:45:10.644127 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis## 2023-10-24 17:45:10.891567 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis## 2023-10-24 17:45:11.120187 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31## 2023-10-24 17:45:11.357009 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae## 2023-10-24 17:45:11.592891 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8## 2023-10-24 17:45:11.821055 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae## 2023-10-24 17:45:12.069171 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii## 2023-10-24 17:45:12.306352 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii## 2023-10-24 17:45:12.543126 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum## 2023-10-24 17:45:12.824649 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA## 2023-10-24 17:45:15.894198 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2023-10-24 17:45:15.896065 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified## 2023-10-24 17:45:16.118005 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii## 2023-10-24 17:45:16.375534 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae## 2023-10-24 17:45:16.62172 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified## 2023-10-24 17:45:16.876194 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis## 2023-10-24 17:45:17.120624 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum## 2023-10-24 17:45:17.379071 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus## 2023-10-24 17:45:17.622041 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis## 2023-10-24 17:45:17.866985 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii## 2023-10-24 17:45:18.138415 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale## 2023-10-24 17:45:18.383693 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis## 2023-10-24 17:45:18.644514 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis## 2023-10-24 17:45:18.899001 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA## 2023-10-24 17:45:19.13835 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii## 2023-10-24 17:45:19.392855 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens## 2023-10-24 17:45:19.645072 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris## 2023-10-24 17:45:19.890493 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii## 2023-10-24 17:45:20.146314 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis## 2023-10-24 17:45:20.38684 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum## 2023-10-24 17:45:20.635607 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus## 2023-10-24 17:45:20.888294 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii## 2023-10-24 17:45:21.130597 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii## 2023-10-24 17:45:21.380607 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae## 2023-10-24 17:45:21.635384 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus## 2023-10-24 17:45:21.875236 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum## 2023-10-24 17:45:22.161268 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae## 2023-10-24 17:45:22.427629 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae## 2023-10-24 17:45:22.661926 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum## 2023-10-24 17:45:22.925469 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis## 2023-10-24 17:45:23.194113 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii## 2023-10-24 17:45:23.459531 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques## 2023-10-24 17:45:23.703467 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8## 2023-10-24 17:45:23.956355 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum## 2023-10-24 17:45:24.208608 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum## 2023-10-24 17:45:24.460722 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis## 2023-10-24 17:45:24.730453 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens## 2023-10-24 17:45:24.983644 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi## 2023-10-24 17:45:25.244216 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified## 2023-10-24 17:45:25.501417 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens## 2023-10-24 17:45:25.748079 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus## 2023-10-24 17:45:26.008665 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae## 2023-10-24 17:45:26.281606 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus## 2023-10-24 17:45:26.540589 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris## 2023-10-24 17:45:26.805402 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47## 2023-10-24 17:45:29.924624 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2023-10-24 17:45:29.926439 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii## 2023-10-24 17:45:30.154978 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale## 2023-10-24 17:45:30.417392 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31## 2023-10-24 17:45:30.664328 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis## 2023-10-24 17:45:30.922145 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified## 2023-10-24 17:45:31.23796 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA## 2023-10-24 17:45:31.494136 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques## 2023-10-24 17:45:31.76261 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum## 2023-10-24 17:45:32.012975 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus## 2023-10-24 17:45:32.269424 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli## 2023-10-24 17:45:32.525516 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum## 2023-10-24 17:45:32.770028 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified## 2023-10-24 17:45:33.035319 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis## 2023-10-24 17:45:33.281113 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens## 2023-10-24 17:45:33.544351 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae## 2023-10-24 17:45:33.807057 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii## 2023-10-24 17:45:34.045349 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus## 2023-10-24 17:45:34.318708 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified## 2023-10-24 17:45:34.601693 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis## 2023-10-24 17:45:34.846264 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii## 2023-10-24 17:45:35.103666 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans## 2023-10-24 17:45:35.349755 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii## 2023-10-24 17:45:35.616645 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified## 2023-10-24 17:45:35.881146 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii## 2023-10-24 17:45:36.12548 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis## 2023-10-24 17:45:36.397601 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri## 2023-10-24 17:45:36.670697 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei## 2023-10-24 17:45:36.908885 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis## 2023-10-24 17:45:37.172938 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii## 2023-10-24 17:45:40.292893 INFO::Plotting data for metadata number 4, antibiotics
## 2023-10-24 17:45:40.294752 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans## 2023-10-24 17:45:40.50749 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis## 2023-10-24 17:45:40.80396 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale## 2023-10-24 17:45:41.059704 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus## 2023-10-24 17:45:41.32738 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis## 2023-10-24 17:45:41.579115 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena## 2023-10-24 17:45:41.827007 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus## 2023-10-24 17:45:42.100331 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii## 2023-10-24 17:45:42.338143 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum## 2023-10-24 17:45:42.59676 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae## 2023-10-24 17:45:42.836739 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis## 2023-10-24 17:45:43.082525 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii## 2023-10-24 17:45:43.336639 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii## 2023-10-24 17:45:43.58233 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified## 2023-10-24 17:45:43.847386 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum## 2023-10-24 17:45:44.082711 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA## 2023-10-24 17:45:44.334999 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii## 2023-10-24 17:45:44.591131 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31## 2023-10-24 17:45:44.823676 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis## 2023-10-24 17:45:45.07285 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii## 2023-10-24 17:45:45.318833 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis## 2023-10-24 17:45:45.570457 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens## 2023-10-24 17:45:45.824439 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens## 2023-10-24 17:45:46.063713 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron## 2023-10-24 17:45:46.320453 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii## 2023-10-24 17:45:46.582469 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae## 2023-10-24 17:45:46.810932 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum## 2023-10-24 17:45:47.075977 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques## 2023-10-24 17:45:47.331315 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum## 2023-10-24 17:45:47.583297 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis## 2023-10-24 17:45:47.857343 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified## 2023-10-24 17:45:48.133216 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar## 2023-10-24 17:45:48.368358 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica## 2023-10-24 17:45:48.624585 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8## 2023-10-24 17:45:48.972422 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile## 2023-10-24 17:45:49.239522 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47## 2023-10-24 17:45:49.534518 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA## 2023-10-24 17:45:49.77241 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila## 2023-10-24 17:45:50.03331 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae## 2023-10-24 17:45:50.298606 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus## 2023-10-24 17:45:53.370279 INFO::Plotting data for metadata number 5, age
## 2023-10-24 17:45:53.372122 INFO::Creating scatter plot for continuous data, age vs Haemophilus.parainfluenzae## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:53.683824 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.pseudocatenulatum## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:54.044103 INFO::Creating scatter plot for continuous data, age vs Faecalibacterium.prausnitzii## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:54.319393 INFO::Creating scatter plot for continuous data, age vs Clostridium.clostridioforme## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:54.611955 INFO::Creating scatter plot for continuous data, age vs Veillonella.parvula## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:54.878519 INFO::Creating scatter plot for continuous data, age vs Subdoligranulum.unclassified## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:55.142134 INFO::Creating scatter plot for continuous data, age vs Clostridium.symbiosum## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:55.432693 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.gnavus## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:55.719101 INFO::Creating scatter plot for continuous data, age vs Dialister.invisus## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:55.999444 INFO::Creating scatter plot for continuous data, age vs Veillonella.dispar## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:56.280036 INFO::Creating scatter plot for continuous data, age vs Veillonella.unclassified## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:56.545809 INFO::Creating scatter plot for continuous data, age vs Bacteroides.thetaiotaomicron## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:56.809259 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.bromii## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:57.092929 INFO::Creating scatter plot for continuous data, age vs Bacteroides.intestinalis## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:57.379814 INFO::Creating scatter plot for continuous data, age vs Eubacterium.siraeum## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:57.938649 INFO::Creating scatter plot for continuous data, age vs Prevotella.copri## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:58.180006 INFO::Creating scatter plot for continuous data, age vs Alistipes.unclassified## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:58.407833 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 (`geom_point()`).## 2023-10-24 17:45:58.649825 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.longum## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:58.886102 INFO::Creating scatter plot for continuous data, age vs Akkermansia.muciniphila## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:59.120379 INFO::Creating scatter plot for continuous data, age vs Collinsella.aerofaciens## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:45:59.358645 INFO::Creating scatter plot for continuous data, age vs Parabacteroides.distasonis## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## `geom_smooth()` using formula = 'y ~ x'## Warning: Removed 19 rows containing missing values (`geom_point()`).## 2023-10-24 17:46:02.355642 INFO::Plotting data for metadata number 6, diagnosis
## 2023-10-24 17:46:02.357371 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis## 2023-10-24 17:46:02.566704 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila## 2023-10-24 17:46:02.811646 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae## 2023-10-24 17:46:03.056983 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis## 2023-10-24 17:46:03.297585 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified## 2023-10-24 17:46:03.540109 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme## 2023-10-24 17:46:03.779708 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii## 2023-10-24 17:46:04.012237 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii## 2023-10-24 17:46:04.256425 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum## 2023-10-24 17:46:04.50071 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum## 2023-10-24 17:46:04.739475 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans## 2023-10-24 17:46:04.982627 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii## 2023-10-24 17:46:05.22991 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii## 2023-10-24 17:46:05.468389 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii## 2023-10-24 17:46:05.717789 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii## 2023-10-24 17:46:06.005858 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified## 2023-10-24 17:46:06.23997 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum## 2023-10-24 17:46:06.493822 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis## 2023-10-24 17:46:06.733561 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified## 2023-10-24 17:46:06.988559 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii## 2023-10-24 17:46:07.24402 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum## 2023-10-24 17:46:07.502984 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis## 2023-10-24 17:46:07.765682 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis## 2023-10-24 17:46:08.007465 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila## 2023-10-24 17:46:08.253097 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis## 2023-10-24 17:46:08.500391 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified## 2023-10-24 17:46:08.735404 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum## 2023-10-24 17:46:08.993434 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii## 2023-10-24 17:46:09.245473 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified## 2023-10-24 17:46:09.487561 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris## 2023-10-24 17:46:09.736264 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus## 2023-10-24 17:46:09.979466 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus## 2023-10-24 17:46:10.214162 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis## 2023-10-24 17:46:10.466853 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale## 2023-10-24 17:46:10.715857 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus## 2023-10-24 17:46:10.958536 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis## 2023-10-24 17:46:11.207364 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale## 2023-10-24 17:46:11.461112 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii## 2023-10-24 17:46:11.709758 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus## 2023-10-24 17:46:11.960679 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii## 2023-10-24 17:46:12.21081 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis## 2023-10-24 17:46:12.453903 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae## 2023-10-24 17:46:12.708735 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.siraeumSession info from running the demo in R can be displayed with the following command.
sessionInfo()## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] Maaslin2_1.16.0
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.4 biglm_0.9-2.1 xfun_0.40
## [4] bslib_0.5.1 ggplot2_3.4.4 lattice_0.22-5
## [7] numDeriv_2016.8-1.1 vctrs_0.6.4 tools_4.3.1
## [10] generics_0.1.3 parallel_4.3.1 getopt_1.20.4
## [13] tibble_3.2.1 fansi_1.0.5 DEoptimR_1.1-3
## [16] cluster_2.1.4 pkgconfig_2.0.3 logging_0.10-108
## [19] pheatmap_1.0.12 Matrix_1.6-1.1 data.table_1.14.8
## [22] RColorBrewer_1.1-3 lifecycle_1.0.3 farver_2.1.1
## [25] compiler_4.3.1 munsell_0.5.0 lmerTest_3.1-3
## [28] permute_0.9-7 htmltools_0.5.6.1 sass_0.4.7
## [31] hash_2.2.6.3 yaml_2.3.7 pillar_1.9.0
## [34] nloptr_2.0.3 crayon_1.5.2 jquerylib_0.1.4
## [37] MASS_7.3-60 cachem_1.0.8 vegan_2.6-4
## [40] boot_1.3-28.1 nlme_3.1-163 robustbase_0.99-0
## [43] tidyselect_1.2.0 digest_0.6.33 mvtnorm_1.2-3
## [46] dplyr_1.1.3 labeling_0.4.3 splines_4.3.1
## [49] pcaPP_2.0-3 fastmap_1.1.1 grid_4.3.1
## [52] colorspace_2.1-0 cli_3.6.1 magrittr_2.0.3
## [55] utf8_1.2.4 withr_2.5.1 scales_1.2.1
## [58] rmarkdown_2.25 lme4_1.1-34 pbapply_1.7-2
## [61] evaluate_0.22 knitr_1.44 mgcv_1.9-0
## [64] rlang_1.1.1 Rcpp_1.0.11 glue_1.6.2
## [67] optparse_1.7.3 DBI_1.1.3 minqa_1.2.6
## [70] jsonlite_1.8.7 R6_2.5.1Run MaAsLin2 help to print a list of the options and the default settings.
$ Maaslin2.R –help Usage: ./R/Maaslin2.R options <data.tsv> <metadata.tsv>
Options: -h, –help Show this help message and exit
-a MIN_ABUNDANCE, --min_abundance=MIN_ABUNDANCE
The minimum abundance for each feature [ Default: 0 ]
-p MIN_PREVALENCE, --min_prevalence=MIN_PREVALENCE
The minimum percent of samples for which a feature
is detected at minimum abundance [ Default: 0.1 ]
-b MIN_VARIANCE, --min_variance=MIN_VARIANCE
Keep features with variance greater than [ Default: 0.0 ]
-s MAX_SIGNIFICANCE, --max_significance=MAX_SIGNIFICANCE
The q-value threshold for significance [ Default: 0.25 ]
-n NORMALIZATION, --normalization=NORMALIZATION
The normalization method to apply [ Default: TSS ]
[ Choices: TSS, CLR, CSS, NONE, TMM ]
-t TRANSFORM, --transform=TRANSFORM
The transform to apply [ Default: LOG ]
[ Choices: LOG, LOGIT, AST, NONE ]
-m ANALYSIS_METHOD, --analysis_method=ANALYSIS_METHOD
The analysis method to apply [ Default: LM ]
[ Choices: LM, CPLM, NEGBIN, ZINB ]
-r RANDOM_EFFECTS, --random_effects=RANDOM_EFFECTS
The random effects for the model, comma-delimited
for multiple effects [ Default: none ]
-f FIXED_EFFECTS, --fixed_effects=FIXED_EFFECTS
The fixed effects for the model, comma-delimited
for multiple effects [ Default: all ]
-c CORRECTION, --correction=CORRECTION
The correction method for computing the
q-value [ Default: BH ]
-z STANDARDIZE, --standardize=STANDARDIZE
Apply z-score so continuous metadata are
on the same scale [ Default: TRUE ]
-l PLOT_HEATMAP, --plot_heatmap=PLOT_HEATMAP
Generate a heatmap for the significant
associations [ Default: TRUE ]
-i HEATMAP_FIRST_N, --heatmap_first_n=HEATMAP_FIRST_N
In heatmap, plot top N features with significant
associations [ Default: TRUE ]
-o PLOT_SCATTER, --plot_scatter=PLOT_SCATTER
Generate scatter plots for the significant
associations [ Default: TRUE ]
-g MAX_PNGS, --max_pngs=MAX_PNGS
The maximum number of scatter plots for signficant associations
to save as png files [ Default: 10 ]
-O SAVE_SCATTER, --save_scatter=SAVE_SCATTER
Save all scatter plot ggplot objects
to an RData file [ Default: FALSE ]
-e CORES, --cores=CORES
The number of R processes to run in parallel
[ Default: 1 ]
-j SAVE_MODELS --save_models=SAVE_MODELS
Return the full model outputs and save to an RData file
[ Default: FALSE ]
-d REFERENCE, --reference=REFERENCE
The factor to use as a reference level for a categorical variable
provided as a string of 'variable,reference', semi-colon delimited for
multiple variables. Not required if metadata is passed as a factor or
for variables with less than two levels but can be set regardless.
[ Default: NA ] Maaslin2.R: command not found. How do I fix this?
Error in library(Maaslin2): there is no package called 'Maaslin2'. How do I fix this?