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"
## 2024-05-04 20:52:00.256771 INFO::Writing function arguments to log file
## 2024-05-04 20:52:00.283977 INFO::Verifying options selected are valid
## 2024-05-04 20:52:00.333011 INFO::Determining format of input files
## 2024-05-04 20:52:00.334633 INFO::Input format is data samples as rows and metadata samples as rows
## 2024-05-04 20:52:00.340333 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2024-05-04 20:52:00.341737 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2024-05-04 20:52:00.344115 INFO::Filter data based on min abundance and min prevalence
## 2024-05-04 20:52:00.344877 INFO::Total samples in data: 1595
## 2024-05-04 20:52:00.345591 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2024-05-04 20:52:00.350485 INFO::Total filtered features: 0
## 2024-05-04 20:52:00.351584 INFO::Filtered feature names from abundance and prevalence filtering:
## 2024-05-04 20:52:00.361048 INFO::Total filtered features with variance filtering: 0
## 2024-05-04 20:52:00.362089 INFO::Filtered feature names from variance filtering:
## 2024-05-04 20:52:00.362749 INFO::Running selected normalization method: TSS
## 2024-05-04 20:52:01.604547 INFO::Bypass z-score application to metadata
## 2024-05-04 20:52:01.606516 INFO::Running selected transform method: LOG
## 2024-05-04 20:52:01.626939 INFO::Running selected analysis method: LM
## 2024-05-04 20:52:01.972354 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:02.381312 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2024-05-04 20:52:02.582268 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2024-05-04 20:52:02.86341 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:03.315496 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2024-05-04 20:52:03.50453 INFO::Fitting model to feature number 6, Bacteroides.caccae
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:03.680228 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2024-05-04 20:52:03.857999 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2024-05-04 20:52:04.057021 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2024-05-04 20:52:04.228394 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2024-05-04 20:52:04.40333 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
## 2024-05-04 20:52:04.543786 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
## 2024-05-04 20:52:04.73637 INFO::Fitting model to feature number 12, Bacteroides.fragilis
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:04.911008 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:05.095275 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2024-05-04 20:52:05.278169 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:05.441132 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2024-05-04 20:52:05.610393 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2024-05-04 20:52:05.780966 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:05.956642 INFO::Fitting model to feature number 19, Bacteroides.uniformis
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:06.126051 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:06.293553 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:06.474461 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2024-05-04 20:52:06.638861 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2024-05-04 20:52:06.810006 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2024-05-04 20:52:06.995339 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2024-05-04 20:52:07.161873 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:07.32517 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2024-05-04 20:52:07.490814 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2024-05-04 20:52:07.669937 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:07.83499 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2024-05-04 20:52:08.01057 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2024-05-04 20:52:08.1847 INFO::Fitting model to feature number 32, Prevotella.copri
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:08.351512 INFO::Fitting model to feature number 33, Alistipes.finegoldii
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:08.514893 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
## 2024-05-04 20:52:08.665346 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
## 2024-05-04 20:52:08.837737 INFO::Fitting model to feature number 35, Alistipes.putredinis
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:09.005602 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2024-05-04 20:52:09.188503 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2024-05-04 20:52:09.35228 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2024-05-04 20:52:09.533517 INFO::Fitting model to feature number 39, Clostridium.bolteae
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:09.705047 INFO::Fitting model to feature number 40, Clostridium.citroniae
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:09.878171 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:10.052351 INFO::Fitting model to feature number 42, Clostridium.hathewayi
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:10.213703 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2024-05-04 20:52:10.406341 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2024-05-04 20:52:10.566607 INFO::Fitting model to feature number 45, Clostridium.symbiosum
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:10.730286 INFO::Fitting model to feature number 46, Flavonifractor.plautii
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:10.913317 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2024-05-04 20:52:11.077809 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2024-05-04 20:52:11.258744 INFO::Fitting model to feature number 49, Eubacterium.rectale
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:11.434356 INFO::Fitting model to feature number 50, Eubacterium.siraeum
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:11.602807 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:11.765176 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:11.929525 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:12.094173 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2024-05-04 20:52:12.267687 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2024-05-04 20:52:12.435418 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2024-05-04 20:52:12.60874 INFO::Fitting model to feature number 57, Dorea.longicatena
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:12.78392 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:12.968431 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:13.148099 INFO::Fitting model to feature number 60, Roseburia.hominis
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:13.32036 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2024-05-04 20:52:13.492746 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:13.706248 INFO::Fitting model to feature number 63, Roseburia.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:13.873777 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2024-05-04 20:52:14.057277 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2024-05-04 20:52:14.252218 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2024-05-04 20:52:14.425666 INFO::Fitting model to feature number 67, Ruminococcus.bromii
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:14.582166 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2024-05-04 20:52:14.744551 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2024-05-04 20:52:14.930734 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:15.099254 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2024-05-04 20:52:15.258251 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2024-05-04 20:52:15.447219 INFO::Fitting model to feature number 73, Dialister.invisus
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:15.616519 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2024-05-04 20:52:15.794041 INFO::Fitting model to feature number 75, Veillonella.dispar
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:15.981587 INFO::Fitting model to feature number 76, Veillonella.parvula
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:16.147604 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2024-05-04 20:52:16.30963 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2024-05-04 20:52:16.490957 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2024-05-04 20:52:16.655087 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2024-05-04 20:52:16.822696 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2024-05-04 20:52:17.019145 INFO::Fitting model to feature number 82, Escherichia.coli
## 2024-05-04 20:52:17.192122 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2024-05-04 20:52:17.352387 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:17.535376 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
## boundary (singular) fit: see help('isSingular')
## 2024-05-04 20:52:17.702656 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2024-05-04 20:52:17.889989 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2024-05-04 20:52:18.106199 INFO::Counting total values for each feature
## 2024-05-04 20:52:18.147117 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2024-05-04 20:52:18.292575 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2024-05-04 20:52:18.463485 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2024-05-04 20:52:18.714407 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2024-05-04 20:52:18.804315 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2024-05-04 20:52:18.853929 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2024-05-04 20:52:18.863444 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2024-05-04 20:52:18.873441 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
## 2024-05-04 20:52:18.87791 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2024-05-04 20:52:19.063546 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2024-05-04 20:52:19.071938 INFO::Plotting associations from most to least significant, grouped by metadata
## 2024-05-04 20:52:19.073214 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2024-05-04 20:52:19.075319 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii
## 2024-05-04 20:52:19.478985 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified
## 2024-05-04 20:52:19.82059 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis
## 2024-05-04 20:52:20.096878 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale
## 2024-05-04 20:52:20.387812 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus
## 2024-05-04 20:52:20.667501 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus
## 2024-05-04 20:52:20.973613 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum
## 2024-05-04 20:52:21.252713 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified
## 2024-05-04 20:52:21.547334 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans
## 2024-05-04 20:52:21.828446 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis
## 2024-05-04 20:52:22.119413 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron
## 2024-05-04 20:52:22.388415 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis
## 2024-05-04 20:52:23.034786 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis
## 2024-05-04 20:52:23.299151 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei
## 2024-05-04 20:52:23.574324 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii
## 2024-05-04 20:52:23.843109 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens
## 2024-05-04 20:52:24.13451 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum
## 2024-05-04 20:52:24.405349 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena
## 2024-05-04 20:52:24.690415 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae
## 2024-05-04 20:52:24.962045 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-05-04 20:52:25.245646 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli
## 2024-05-04 20:52:25.515473 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae
## 2024-05-04 20:52:25.791543 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified
## 2024-05-04 20:52:26.045558 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii
## 2024-05-04 20:52:26.357586 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens
## 2024-05-04 20:52:26.627361 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris
## 2024-05-04 20:52:26.90648 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes
## 2024-05-04 20:52:27.161331 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis
## 2024-05-04 20:52:27.434818 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii
## 2024-05-04 20:52:27.705471 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii
## 2024-05-04 20:52:27.97835 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis
## 2024-05-04 20:52:28.249647 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara
## 2024-05-04 20:52:28.528272 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum
## 2024-05-04 20:52:28.786745 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae
## 2024-05-04 20:52:29.069876 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified
## 2024-05-04 20:52:29.339475 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens
## 2024-05-04 20:52:29.627863 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus
## 2024-05-04 20:52:29.905702 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme
## 2024-05-04 20:52:30.194458 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii
## 2024-05-04 20:52:30.464039 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii
## 2024-05-04 20:52:30.746086 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum
## 2024-05-04 20:52:31.022442 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris
## 2024-05-04 20:52:31.307957 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47
## 2024-05-04 20:52:31.569519 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus
## 2024-05-04 20:52:31.849167 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii
## 2024-05-04 20:52:32.117058 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis
## 2024-05-04 20:52:32.38976 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified
## 2024-05-04 20:52:32.667226 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques
## 2024-05-04 20:52:32.922634 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified
## 2024-05-04 20:52:33.218188 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus
## 2024-05-04 20:52:33.479408 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis
## 2024-05-04 20:52:33.7556 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified
## 2024-05-04 20:52:34.016014 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified
## 2024-05-04 20:52:34.288746 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis
## 2024-05-04 20:52:34.56103 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis
## 2024-05-04 20:52:34.840637 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31
## 2024-05-04 20:52:35.107877 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae
## 2024-05-04 20:52:35.390347 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8
## 2024-05-04 20:52:35.653087 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae
## 2024-05-04 20:52:35.939071 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii
## 2024-05-04 20:52:36.248848 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii
## 2024-05-04 20:52:36.562639 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum
## 2024-05-04 20:52:36.828846 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-05-04 20:52:39.900832 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2024-05-04 20:52:39.903608 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified
## 2024-05-04 20:52:40.138106 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii
## 2024-05-04 20:52:40.462071 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae
## 2024-05-04 20:52:40.757614 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified
## 2024-05-04 20:52:41.073286 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis
## 2024-05-04 20:52:41.361731 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum
## 2024-05-04 20:52:41.669798 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus
## 2024-05-04 20:52:41.933828 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis
## 2024-05-04 20:52:42.240045 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii
## 2024-05-04 20:52:42.511057 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale
## 2024-05-04 20:52:42.814406 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis
## 2024-05-04 20:52:43.09834 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis
## 2024-05-04 20:52:43.403595 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-05-04 20:52:43.678778 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii
## 2024-05-04 20:52:43.96992 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens
## 2024-05-04 20:52:44.236555 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris
## 2024-05-04 20:52:44.539299 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii
## 2024-05-04 20:52:44.812859 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis
## 2024-05-04 20:52:45.113347 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum
## 2024-05-04 20:52:45.369817 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus
## 2024-05-04 20:52:45.666564 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii
## 2024-05-04 20:52:45.933398 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii
## 2024-05-04 20:52:46.234704 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae
## 2024-05-04 20:52:46.52533 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus
## 2024-05-04 20:52:46.795267 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum
## 2024-05-04 20:52:47.074739 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae
## 2024-05-04 20:52:47.349415 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae
## 2024-05-04 20:52:47.641586 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum
## 2024-05-04 20:52:47.90875 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis
## 2024-05-04 20:52:48.207774 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii
## 2024-05-04 20:52:48.476096 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques
## 2024-05-04 20:52:48.755197 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8
## 2024-05-04 20:52:49.036765 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum
## 2024-05-04 20:52:49.42216 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum
## 2024-05-04 20:52:49.724526 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis
## 2024-05-04 20:52:50.034666 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens
## 2024-05-04 20:52:50.322842 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi
## 2024-05-04 20:52:50.635019 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified
## 2024-05-04 20:52:50.915585 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens
## 2024-05-04 20:52:51.220574 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus
## 2024-05-04 20:52:51.490722 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae
## 2024-05-04 20:52:51.797608 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus
## 2024-05-04 20:52:52.087511 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris
## 2024-05-04 20:52:52.378303 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47
## 2024-05-04 20:52:55.212736 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2024-05-04 20:52:55.215433 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii
## 2024-05-04 20:52:55.449969 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale
## 2024-05-04 20:52:55.729607 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31
## 2024-05-04 20:52:56.028011 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis
## 2024-05-04 20:52:56.293298 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified
## 2024-05-04 20:52:56.591782 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-05-04 20:52:56.878416 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques
## 2024-05-04 20:52:57.180353 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum
## 2024-05-04 20:52:57.468307 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus
## 2024-05-04 20:52:57.767166 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli
## 2024-05-04 20:52:58.039144 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum
## 2024-05-04 20:52:58.369192 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified
## 2024-05-04 20:52:58.679036 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis
## 2024-05-04 20:52:58.960895 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens
## 2024-05-04 20:52:59.274007 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae
## 2024-05-04 20:52:59.549959 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii
## 2024-05-04 20:52:59.826829 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus
## 2024-05-04 20:53:00.095103 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified
## 2024-05-04 20:53:00.405883 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis
## 2024-05-04 20:53:00.665925 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii
## 2024-05-04 20:53:01.050505 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans
## 2024-05-04 20:53:01.333206 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii
## 2024-05-04 20:53:01.646148 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified
## 2024-05-04 20:53:01.922513 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii
## 2024-05-04 20:53:02.227707 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis
## 2024-05-04 20:53:02.505294 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri
## 2024-05-04 20:53:02.831455 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei
## 2024-05-04 20:53:03.12152 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis
## 2024-05-04 20:53:03.429236 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii
## 2024-05-04 20:53:06.384478 INFO::Plotting data for metadata number 4, antibiotics
## 2024-05-04 20:53:06.38723 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans
## 2024-05-04 20:53:06.636182 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis
## 2024-05-04 20:53:06.912152 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale
## 2024-05-04 20:53:07.210599 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus
## 2024-05-04 20:53:07.479714 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis
## 2024-05-04 20:53:07.778878 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena
## 2024-05-04 20:53:08.053053 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus
## 2024-05-04 20:53:08.365272 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii
## 2024-05-04 20:53:08.614613 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum
## 2024-05-04 20:53:08.923166 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae
## 2024-05-04 20:53:09.198795 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis
## 2024-05-04 20:53:09.482427 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii
## 2024-05-04 20:53:09.743646 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii
## 2024-05-04 20:53:10.048763 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified
## 2024-05-04 20:53:10.315878 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum
## 2024-05-04 20:53:10.613428 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA
## 2024-05-04 20:53:10.876514 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii
## 2024-05-04 20:53:11.179125 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31
## 2024-05-04 20:53:11.441404 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis
## 2024-05-04 20:53:11.741107 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii
## 2024-05-04 20:53:12.00565 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis
## 2024-05-04 20:53:12.305538 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens
## 2024-05-04 20:53:12.561777 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens
## 2024-05-04 20:53:12.968608 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron
## 2024-05-04 20:53:13.250721 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii
## 2024-05-04 20:53:13.563761 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae
## 2024-05-04 20:53:13.831795 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum
## 2024-05-04 20:53:14.138263 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques
## 2024-05-04 20:53:14.39814 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum
## 2024-05-04 20:53:14.711126 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis
## 2024-05-04 20:53:14.981501 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified
## 2024-05-04 20:53:15.285373 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar
## 2024-05-04 20:53:15.54927 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica
## 2024-05-04 20:53:15.853606 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8
## 2024-05-04 20:53:16.11334 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile
## 2024-05-04 20:53:16.409981 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47
## 2024-05-04 20:53:16.697146 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA
## 2024-05-04 20:53:17.000852 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila
## 2024-05-04 20:53:17.267103 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae
## 2024-05-04 20:53:17.564413 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus
## 2024-05-04 20:53:20.451542 INFO::Plotting data for metadata number 5, age
## 2024-05-04 20:53:20.454138 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()`).
## 2024-05-04 20:53:20.742702 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()`).
## 2024-05-04 20:53:21.13549 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()`).
## 2024-05-04 20:53:21.425579 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()`).
## 2024-05-04 20:53:21.751214 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()`).
## 2024-05-04 20:53:22.010879 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()`).
## 2024-05-04 20:53:22.305684 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()`).
## 2024-05-04 20:53:22.606842 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()`).
## 2024-05-04 20:53:22.87414 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()`).
## 2024-05-04 20:53:23.172762 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()`).
## 2024-05-04 20:53:23.457498 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()`).
## 2024-05-04 20:53:23.73371 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()`).
## 2024-05-04 20:53:24.452549 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()`).
## 2024-05-04 20:53:24.706067 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()`).
## 2024-05-04 20:53:24.965893 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()`).
## 2024-05-04 20:53:25.205157 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()`).
## 2024-05-04 20:53:25.45567 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()`).
## 2024-05-04 20:53:25.635693 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()`).
## 2024-05-04 20:53:25.794035 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()`).
## 2024-05-04 20:53:25.983635 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()`).
## 2024-05-04 20:53:26.18585 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()`).
## 2024-05-04 20:53:26.375181 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()`).
## 2024-05-04 20:53:29.095483 INFO::Plotting data for metadata number 6, diagnosis
## 2024-05-04 20:53:29.09824 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis
## 2024-05-04 20:53:29.309841 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-05-04 20:53:29.589526 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-05-04 20:53:29.85412 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-05-04 20:53:30.145934 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-05-04 20:53:30.41651 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme
## 2024-05-04 20:53:30.701352 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-05-04 20:53:30.963012 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-05-04 20:53:31.232841 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-05-04 20:53:31.485229 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-05-04 20:53:31.751838 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans
## 2024-05-04 20:53:32.022345 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii
## 2024-05-04 20:53:32.288994 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii
## 2024-05-04 20:53:32.567149 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-05-04 20:53:32.842121 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii
## 2024-05-04 20:53:33.11694 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified
## 2024-05-04 20:53:33.362762 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum
## 2024-05-04 20:53:33.634641 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-05-04 20:53:33.893863 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified
## 2024-05-04 20:53:34.270365 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-05-04 20:53:34.554021 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum
## 2024-05-04 20:53:34.85244 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis
## 2024-05-04 20:53:35.137126 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-05-04 20:53:35.420086 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila
## 2024-05-04 20:53:35.711504 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis
## 2024-05-04 20:53:35.981351 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified
## 2024-05-04 20:53:36.268747 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum
## 2024-05-04 20:53:36.555861 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii
## 2024-05-04 20:53:36.855697 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
## 2024-05-04 20:53:37.143318 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris
## 2024-05-04 20:53:37.439561 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-05-04 20:53:37.731643 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus
## 2024-05-04 20:53:38.019432 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis
## 2024-05-04 20:53:38.300893 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-05-04 20:53:38.59861 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus
## 2024-05-04 20:53:38.887478 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis
## 2024-05-04 20:53:39.179096 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale
## 2024-05-04 20:53:39.463361 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii
## 2024-05-04 20:53:39.773802 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus
## 2024-05-04 20:53:40.058966 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii
## 2024-05-04 20:53:40.328465 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis
## 2024-05-04 20:53:40.62636 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae
## 2024-05-04 20:53:40.90461 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_1.19.0
##
## 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?