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"
## 2024-05-01 17:56:06.245594 INFO::Writing function arguments to log file
## 2024-05-01 17:56:06.274901 INFO::Verifying options selected are valid
## 2024-05-01 17:56:06.308906 INFO::Determining format of input files
## 2024-05-01 17:56:06.310005 INFO::Input format is data samples as rows and metadata samples as rows
## 2024-05-01 17:56:06.313903 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2024-05-01 17:56:06.314928 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2024-05-01 17:56:06.31705 INFO::Filter data based on min abundance and min prevalence
## 2024-05-01 17:56:06.317673 INFO::Total samples in data: 1595
## 2024-05-01 17:56:06.31827 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2024-05-01 17:56:06.322825 INFO::Total filtered features: 0
## 2024-05-01 17:56:06.32362 INFO::Filtered feature names from abundance and prevalence filtering:
## 2024-05-01 17:56:06.332319 INFO::Total filtered features with variance filtering: 0
## 2024-05-01 17:56:06.333086 INFO::Filtered feature names from variance filtering:
## 2024-05-01 17:56:06.333703 INFO::Running selected normalization method: TSS
## 2024-05-01 17:56:07.383992 INFO::Bypass z-score application to metadata
## 2024-05-01 17:56:07.384989 INFO::Running selected transform method: LOG
## 2024-05-01 17:56:07.400712 INFO::Running selected analysis method: LM
## 2024-05-01 17:56:07.678406 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:07.989255 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2024-05-01 17:56:08.204499 INFO::Fitting model to feature number 3, Bifidobacterium.longum
## 2024-05-01 17:56:08.527934 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:08.656748 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2024-05-01 17:56:08.811054 INFO::Fitting model to feature number 6, Bacteroides.caccae## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:08.959184 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2024-05-01 17:56:09.102077 INFO::Fitting model to feature number 8, Bacteroides.dorei
## 2024-05-01 17:56:09.24265 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
## 2024-05-01 17:56:09.376322 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2024-05-01 17:56:09.513211 INFO::Fitting model to feature number 11, Bacteroides.finegoldii## boundary (singular) fit: see help('isSingular')## Feature Bacteroides.finegoldii : simpleWarning: Model failed to converge with 1 negative eigenvalue: -7.9e+01## 2024-05-01 17:56:09.627353 WARNING::Fitting problem for feature 11 a warning was issued## boundary (singular) fit: see help('isSingular')## Warning: Model failed to converge with 1 negative eigenvalue: -7.9e+01## 2024-05-01 17:56:09.759974 INFO::Fitting model to feature number 12, Bacteroides.fragilis## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:09.890356 INFO::Fitting model to feature number 13, Bacteroides.intestinalis## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:10.029785 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
## 2024-05-01 17:56:10.159371 INFO::Fitting model to feature number 15, Bacteroides.ovatus## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:10.285658 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
## 2024-05-01 17:56:10.424412 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2024-05-01 17:56:10.556365 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:10.684921 INFO::Fitting model to feature number 19, Bacteroides.uniformis## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:10.815099 INFO::Fitting model to feature number 20, Bacteroides.vulgatus## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:10.950602 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:11.081028 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2024-05-01 17:56:11.220939 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2024-05-01 17:56:11.383256 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2024-05-01 17:56:11.53133 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
## 2024-05-01 17:56:11.667067 INFO::Fitting model to feature number 26, Parabacteroides.distasonis## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:11.805936 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2024-05-01 17:56:11.940958 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2024-05-01 17:56:12.076489 INFO::Fitting model to feature number 29, Parabacteroides.unclassified## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:12.212703 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2024-05-01 17:56:12.349862 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2024-05-01 17:56:12.483681 INFO::Fitting model to feature number 32, Prevotella.copri## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:12.619498 INFO::Fitting model to feature number 33, Alistipes.finegoldii## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:12.748682 INFO::Fitting model to feature number 34, Alistipes.onderdonkii## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:12.889392 INFO::Fitting model to feature number 35, Alistipes.putredinis## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:13.020651 INFO::Fitting model to feature number 36, Alistipes.shahii
## 2024-05-01 17:56:13.157256 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2024-05-01 17:56:13.291931 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2024-05-01 17:56:13.430289 INFO::Fitting model to feature number 39, Clostridium.bolteae## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:13.574521 INFO::Fitting model to feature number 40, Clostridium.citroniae## boundary (singular) fit: see help('isSingular')## Feature Clostridium.citroniae : simpleWarning: Model failed to converge with 1 negative eigenvalue: -3.4e+01## 2024-05-01 17:56:13.691489 WARNING::Fitting problem for feature 40 a warning was issued## boundary (singular) fit: see help('isSingular')## Warning: Model failed to converge with 1 negative eigenvalue: -3.4e+01## 2024-05-01 17:56:13.825054 INFO::Fitting model to feature number 41, Clostridium.clostridioforme## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:13.960582 INFO::Fitting model to feature number 42, Clostridium.hathewayi## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:14.094553 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2024-05-01 17:56:14.246892 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2024-05-01 17:56:14.385279 INFO::Fitting model to feature number 45, Clostridium.symbiosum## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:14.518175 INFO::Fitting model to feature number 46, Flavonifractor.plautii## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:14.658818 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2024-05-01 17:56:14.79137 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2024-05-01 17:56:14.938873 INFO::Fitting model to feature number 49, Eubacterium.rectale## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:15.080375 INFO::Fitting model to feature number 50, Eubacterium.siraeum## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:15.220207 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:15.355896 INFO::Fitting model to feature number 52, Eubacterium.ventriosum## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:15.49068 INFO::Fitting model to feature number 53, Ruminococcus.gnavus## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:15.625046 INFO::Fitting model to feature number 54, Ruminococcus.obeum
## 2024-05-01 17:56:15.759348 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2024-05-01 17:56:15.891715 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2024-05-01 17:56:16.049953 INFO::Fitting model to feature number 57, Dorea.longicatena## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:16.20882 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:16.347435 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:16.506665 INFO::Fitting model to feature number 60, Roseburia.hominis## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:16.645452 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2024-05-01 17:56:16.778671 INFO::Fitting model to feature number 62, Roseburia.inulinivorans## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:16.925224 INFO::Fitting model to feature number 63, Roseburia.unclassified## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:17.059269 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2024-05-01 17:56:17.206881 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
## 2024-05-01 17:56:17.344293 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2024-05-01 17:56:17.486804 INFO::Fitting model to feature number 67, Ruminococcus.bromii## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:17.613608 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2024-05-01 17:56:17.745669 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2024-05-01 17:56:17.889325 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:18.021675 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2024-05-01 17:56:18.150343 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
## 2024-05-01 17:56:18.291736 INFO::Fitting model to feature number 73, Dialister.invisus## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:18.421595 INFO::Fitting model to feature number 74, Veillonella.atypica
## 2024-05-01 17:56:18.562201 INFO::Fitting model to feature number 75, Veillonella.dispar## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:18.708622 INFO::Fitting model to feature number 76, Veillonella.parvula## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:18.83898 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2024-05-01 17:56:18.973919 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2024-05-01 17:56:19.11343 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
## 2024-05-01 17:56:19.24214 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2024-05-01 17:56:19.378154 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2024-05-01 17:56:19.524855 INFO::Fitting model to feature number 82, Escherichia.coli
## 2024-05-01 17:56:19.660428 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2024-05-01 17:56:19.791548 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:19.918777 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae## boundary (singular) fit: see help('isSingular')## 2024-05-01 17:56:20.053682 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
## 2024-05-01 17:56:20.195378 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2024-05-01 17:56:20.370474 INFO::Counting total values for each feature
## 2024-05-01 17:56:20.409424 INFO::Writing filtered data to file demo_output/features/filtered_data.tsv
## 2024-05-01 17:56:20.553182 INFO::Writing filtered, normalized data to file demo_output/features/filtered_data_norm.tsv
## 2024-05-01 17:56:20.701975 INFO::Writing filtered, normalized, transformed data to file demo_output/features/filtered_data_norm_transformed.tsv
## 2024-05-01 17:56:20.932942 INFO::Writing residuals to file demo_output/fits/residuals.rds
## 2024-05-01 17:56:20.995381 INFO::Writing fitted values to file demo_output/fits/fitted.rds
## 2024-05-01 17:56:21.030897 INFO::Writing extracted random effects to file demo_output/fits/ranef.rds
## 2024-05-01 17:56:21.036278 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2024-05-01 17:56:21.042513 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
## 2024-05-01 17:56:21.045398 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf
## 2024-05-01 17:56:21.263913 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2024-05-01 17:56:21.269542 INFO::Plotting associations from most to least significant, grouped by metadata
## 2024-05-01 17:56:21.270411 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2024-05-01 17:56:21.271837 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii## 2024-05-01 17:56:21.616982 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified## 2024-05-01 17:56:21.883584 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis## 2024-05-01 17:56:22.144297 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale## 2024-05-01 17:56:22.415285 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus## 2024-05-01 17:56:22.65363 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus## 2024-05-01 17:56:22.895571 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum## 2024-05-01 17:56:23.137164 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified## 2024-05-01 17:56:23.374454 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans## 2024-05-01 17:56:23.871669 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis## 2024-05-01 17:56:24.097948 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron## 2024-05-01 17:56:24.333143 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis## 2024-05-01 17:56:24.560097 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis## 2024-05-01 17:56:24.795348 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.dorei## 2024-05-01 17:56:25.020855 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii## 2024-05-01 17:56:25.253587 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens## 2024-05-01 17:56:25.49365 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum## 2024-05-01 17:56:25.740269 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena## 2024-05-01 17:56:25.974256 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae## 2024-05-01 17:56:26.210097 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-05-01 17:56:26.434816 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli## 2024-05-01 17:56:26.694817 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae## 2024-05-01 17:56:26.926815 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified## 2024-05-01 17:56:27.162036 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii## 2024-05-01 17:56:27.394408 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.eligens## 2024-05-01 17:56:27.633583 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris## 2024-05-01 17:56:27.861791 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes## 2024-05-01 17:56:28.100037 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.fragilis## 2024-05-01 17:56:28.329075 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii## 2024-05-01 17:56:28.557773 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii## 2024-05-01 17:56:28.78779 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis## 2024-05-01 17:56:29.018607 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara## 2024-05-01 17:56:29.246977 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum## 2024-05-01 17:56:29.468397 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae## 2024-05-01 17:56:29.699762 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified## 2024-05-01 17:56:29.948455 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens## 2024-05-01 17:56:30.196647 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus## 2024-05-01 17:56:30.430623 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme## 2024-05-01 17:56:30.661998 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii## 2024-05-01 17:56:30.893113 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.onderdonkii## 2024-05-01 17:56:31.12132 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum## 2024-05-01 17:56:31.353417 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris## 2024-05-01 17:56:31.585013 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47## 2024-05-01 17:56:31.806591 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus## 2024-05-01 17:56:32.038045 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii## 2024-05-01 17:56:32.27358 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis## 2024-05-01 17:56:32.493492 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified## 2024-05-01 17:56:32.730943 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques## 2024-05-01 17:56:32.948327 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified## 2024-05-01 17:56:33.194118 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.cellulosilyticus## 2024-05-01 17:56:33.417815 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.intestinalis## 2024-05-01 17:56:33.655209 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified## 2024-05-01 17:56:33.881717 INFO::Creating boxplot for categorical data, dysbiosisCD vs Acidaminococcus.unclassified## 2024-05-01 17:56:34.116685 INFO::Creating boxplot for categorical data, dysbiosisCD vs Barnesiella.intestinihominis## 2024-05-01 17:56:34.353482 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.massiliensis## 2024-05-01 17:56:34.606199 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.sp.3.1.31## 2024-05-01 17:56:34.830702 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.salyersiae## 2024-05-01 17:56:35.059147 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroidales.bacterium.ph8## 2024-05-01 17:56:35.279283 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.citroniae## 2024-05-01 17:56:35.5134 INFO::Creating boxplot for categorical data, dysbiosisCD vs Flavonifractor.plautii## 2024-05-01 17:56:35.738455 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.goldsteinii## 2024-05-01 17:56:35.972388 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum## 2024-05-01 17:56:36.196629 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.1.1.57FAA## 2024-05-01 17:56:39.160265 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2024-05-01 17:56:39.161912 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified## 2024-05-01 17:56:39.375553 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii## 2024-05-01 17:56:39.611299 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae## 2024-05-01 17:56:39.863751 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified## 2024-05-01 17:56:40.122495 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis## 2024-05-01 17:56:40.381625 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum## 2024-05-01 17:56:40.614728 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus## 2024-05-01 17:56:40.851273 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis## 2024-05-01 17:56:41.085874 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii## 2024-05-01 17:56:41.328738 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale## 2024-05-01 17:56:41.558309 INFO::Creating boxplot for categorical data, dysbiosisUC vs Roseburia.hominis## 2024-05-01 17:56:41.812037 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis## 2024-05-01 17:56:42.044533 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-05-01 17:56:42.291219 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii## 2024-05-01 17:56:42.526394 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens## 2024-05-01 17:56:42.77546 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris## 2024-05-01 17:56:43.010166 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.finegoldii## 2024-05-01 17:56:43.254856 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis## 2024-05-01 17:56:43.485141 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum## 2024-05-01 17:56:43.725745 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus## 2024-05-01 17:56:43.958599 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.onderdonkii## 2024-05-01 17:56:44.208342 INFO::Creating boxplot for categorical data, dysbiosisUC vs Flavonifractor.plautii## 2024-05-01 17:56:44.441475 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.merdae## 2024-05-01 17:56:44.686491 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.cellulosilyticus## 2024-05-01 17:56:44.919577 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.longum## 2024-05-01 17:56:45.161766 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae## 2024-05-01 17:56:45.411011 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.citroniae## 2024-05-01 17:56:45.638876 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum## 2024-05-01 17:56:45.90288 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.distasonis## 2024-05-01 17:56:46.133614 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii## 2024-05-01 17:56:46.377337 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.torques## 2024-05-01 17:56:46.600694 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroidales.bacterium.ph8## 2024-05-01 17:56:46.903673 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum## 2024-05-01 17:56:47.137322 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.bifidum## 2024-05-01 17:56:47.39225 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis## 2024-05-01 17:56:47.62402 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens## 2024-05-01 17:56:47.865314 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.hathewayi## 2024-05-01 17:56:48.098937 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bilophila.unclassified## 2024-05-01 17:56:48.340705 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.eligens## 2024-05-01 17:56:48.572512 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.vulgatus## 2024-05-01 17:56:48.816581 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.bolteae## 2024-05-01 17:56:49.053413 INFO::Creating boxplot for categorical data, dysbiosisUC vs Dialister.invisus## 2024-05-01 17:56:49.300543 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.lactaris## 2024-05-01 17:56:49.536693 INFO::Creating boxplot for categorical data, dysbiosisUC vs Burkholderiales.bacterium.1.1.47## 2024-05-01 17:56:52.453062 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2024-05-01 17:56:52.454825 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii## 2024-05-01 17:56:52.67074 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale## 2024-05-01 17:56:52.905665 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31## 2024-05-01 17:56:53.169956 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis## 2024-05-01 17:56:53.410771 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified## 2024-05-01 17:56:53.665582 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-05-01 17:56:53.90376 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques## 2024-05-01 17:56:54.14937 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum## 2024-05-01 17:56:54.39295 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus## 2024-05-01 17:56:54.636996 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli## 2024-05-01 17:56:54.875538 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum## 2024-05-01 17:56:55.111351 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified## 2024-05-01 17:56:55.364538 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.uniformis## 2024-05-01 17:56:55.599635 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens## 2024-05-01 17:56:55.846894 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae## 2024-05-01 17:56:56.081661 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii## 2024-05-01 17:56:56.316879 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.vulgatus## 2024-05-01 17:56:56.545385 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs C2likevirus.unclassified## 2024-05-01 17:56:56.793676 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bifidobacterium.adolescentis## 2024-05-01 17:56:57.024196 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.finegoldii## 2024-05-01 17:56:57.299006 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.inulinivorans## 2024-05-01 17:56:57.536129 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.onderdonkii## 2024-05-01 17:56:57.787948 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.unclassified## 2024-05-01 17:56:58.025282 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.hallii## 2024-05-01 17:56:58.271295 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.intestinalis## 2024-05-01 17:56:58.511716 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri## 2024-05-01 17:56:58.763427 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.dorei## 2024-05-01 17:56:58.991489 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis## 2024-05-01 17:56:59.243706 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii## 2024-05-01 17:57:02.244327 INFO::Plotting data for metadata number 4, antibiotics
## 2024-05-01 17:57:02.246054 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans## 2024-05-01 17:57:02.448147 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis## 2024-05-01 17:57:02.678413 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale## 2024-05-01 17:57:02.902612 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus## 2024-05-01 17:57:03.146996 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis## 2024-05-01 17:57:03.367275 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena## 2024-05-01 17:57:03.606179 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus## 2024-05-01 17:57:03.831199 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii## 2024-05-01 17:57:04.062884 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum## 2024-05-01 17:57:04.285234 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae## 2024-05-01 17:57:04.523082 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis## 2024-05-01 17:57:04.73785 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii## 2024-05-01 17:57:04.971823 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.hallii## 2024-05-01 17:57:05.200401 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified## 2024-05-01 17:57:05.438828 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.leptum## 2024-05-01 17:57:05.658959 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.3.1.46FAA## 2024-05-01 17:57:05.895504 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii## 2024-05-01 17:57:06.120688 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31## 2024-05-01 17:57:06.356266 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis## 2024-05-01 17:57:06.576347 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii## 2024-05-01 17:57:06.814829 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis## 2024-05-01 17:57:07.036883 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens## 2024-05-01 17:57:07.268386 INFO::Creating boxplot for categorical data, antibiotics vs Collinsella.aerofaciens## 2024-05-01 17:57:07.548934 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron## 2024-05-01 17:57:07.778823 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.eggerthii## 2024-05-01 17:57:08.011511 INFO::Creating boxplot for categorical data, antibiotics vs Haemophilus.parainfluenzae## 2024-05-01 17:57:08.245298 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum## 2024-05-01 17:57:08.474881 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.torques## 2024-05-01 17:57:08.708823 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.ventriosum## 2024-05-01 17:57:08.942596 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis## 2024-05-01 17:57:09.183308 INFO::Creating boxplot for categorical data, antibiotics vs Peptostreptococcaceae.noname.unclassified## 2024-05-01 17:57:09.417166 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.dispar## 2024-05-01 17:57:09.65576 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.atypica## 2024-05-01 17:57:09.884162 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8## 2024-05-01 17:57:10.124216 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.nexile## 2024-05-01 17:57:10.371661 INFO::Creating boxplot for categorical data, antibiotics vs Burkholderiales.bacterium.1.1.47## 2024-05-01 17:57:10.619277 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA## 2024-05-01 17:57:10.844382 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila## 2024-05-01 17:57:11.090114 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.citroniae## 2024-05-01 17:57:11.311296 INFO::Creating boxplot for categorical data, antibiotics vs Odoribacter.splanchnicus## 2024-05-01 17:57:14.150389 INFO::Plotting data for metadata number 5, age
## 2024-05-01 17:57:14.152098 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()`).## 2024-05-01 17:57:14.428586 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()`).## 2024-05-01 17:57:14.747678 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()`).## 2024-05-01 17:57:14.976836 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()`).## 2024-05-01 17:57:15.236973 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()`).## 2024-05-01 17:57:15.461602 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()`).## 2024-05-01 17:57:15.702774 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()`).## 2024-05-01 17:57:15.957385 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()`).## 2024-05-01 17:57:16.183778 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()`).## 2024-05-01 17:57:16.424371 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()`).## 2024-05-01 17:57:16.667784 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()`).## 2024-05-01 17:57:16.8908 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()`).## 2024-05-01 17:57:17.136825 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()`).## 2024-05-01 17:57:17.681861 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()`).## 2024-05-01 17:57:17.893247 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()`).## 2024-05-01 17:57:18.107524 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()`).## 2024-05-01 17:57:18.320279 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()`).## 2024-05-01 17:57:18.536423 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()`).## 2024-05-01 17:57:18.744427 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()`).## 2024-05-01 17:57:18.960871 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()`).## 2024-05-01 17:57:19.177472 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()`).## 2024-05-01 17:57:19.397408 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()`).## 2024-05-01 17:57:22.197986 INFO::Plotting data for metadata number 6, diagnosis
## 2024-05-01 17:57:22.199696 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis## 2024-05-01 17:57:22.404802 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila## 2024-05-01 17:57:22.636881 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae## 2024-05-01 17:57:22.8567 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis## 2024-05-01 17:57:23.097794 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified## 2024-05-01 17:57:23.322163 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme## 2024-05-01 17:57:23.552537 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii## 2024-05-01 17:57:23.776646 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii## 2024-05-01 17:57:24.012908 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum## 2024-05-01 17:57:24.240276 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum## 2024-05-01 17:57:24.473656 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.inulinivorans## 2024-05-01 17:57:24.698658 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii## 2024-05-01 17:57:24.936225 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii## 2024-05-01 17:57:25.157594 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii## 2024-05-01 17:57:25.389177 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii## 2024-05-01 17:57:25.614739 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified## 2024-05-01 17:57:25.842415 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum## 2024-05-01 17:57:26.078472 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis## 2024-05-01 17:57:26.307099 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified## 2024-05-01 17:57:26.546706 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii## 2024-05-01 17:57:26.774718 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.ventriosum## 2024-05-01 17:57:27.061468 INFO::Creating boxplot for categorical data, diagnosis vs Roseburia.hominis## 2024-05-01 17:57:27.297705 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis## 2024-05-01 17:57:27.549449 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila## 2024-05-01 17:57:27.777511 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis## 2024-05-01 17:57:28.017395 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified## 2024-05-01 17:57:28.243152 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.symbiosum## 2024-05-01 17:57:28.490644 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.onderdonkii## 2024-05-01 17:57:28.718905 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified## 2024-05-01 17:57:28.960503 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris## 2024-05-01 17:57:29.187973 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus## 2024-05-01 17:57:29.427822 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus## 2024-05-01 17:57:29.655485 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis## 2024-05-01 17:57:29.901367 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale## 2024-05-01 17:57:30.130714 INFO::Creating boxplot for categorical data, diagnosis vs Odoribacter.splanchnicus## 2024-05-01 17:57:30.37588 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.distasonis## 2024-05-01 17:57:30.60451 INFO::Creating boxplot for categorical data, diagnosis vs Eubacterium.rectale## 2024-05-01 17:57:30.849864 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.finegoldii## 2024-05-01 17:57:31.08175 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus## 2024-05-01 17:57:31.315484 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii## 2024-05-01 17:57:31.550423 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis## 2024-05-01 17:57:31.781238 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae## 2024-05-01 17:57:32.025001 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 4.4.0 RC (2024-04-16 r86468)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.20-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_1.19.0
##
## 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_2.5.1Run 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?