maaslin2
Himel Mallick
himel.stat.iitk@gmail.comAli Rahnavard
gholamali.rahnavard@gmail.comLauren McIver
lauren.j.mciver@gmail.comFriday, May 10, 2019
MaAsLin2 User Manual
MaAsLin2 is the next generation of MaAsLin.
MaAsLin2 is comprehensive R package for finding multivariable association between clinical metadata and microbial meta-omics features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including multiple analysis methods (with support for multiple covariates and repeated measures), filtering, normalization, and transform options to customize analysis for your specific study.
If you use the MaAsLin2 software, please cite our manuscript: Mallick et al. (2020+). “Multivariable Association in Population-scale Meta-omics Studies” (In Preparation).
If you have questions, please email the google group MaAsLin Users.
Contents
Description
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.
Requirements
MaAsLin2 is an R package that can be run on the command line or as an R function.
Installation
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.
From command line
- Download the source: MaAsLin2.tar.gz
- Decompress the download:
$ tar xzvf maaslin2.tar.gz
- Install the Bioconductor dependencies edgeR and metagenomeSeq.
- Install the CRAN dependencies:
$ R -q -e "install.packages(c('lmerTest','pbapply','car','dplyr','vegan','chemometrics','ggplot2','pheatmap','hash','logging','data.table','MuMIn','glmmTMB','MASS','cplm','pscl'), repos='http://cran.r-project.org')"
- Install the MaAsLin2 package (only r,equired if running as an R function):
$ R CMD INSTALL maaslin2
From R
Install Bioconductor and then install Maaslin2
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Maaslin2")How to Run
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.
Input Files
MaAsLin2 requires two input files.
- Data (or features) file
- This file is tab-delimited.
- Formatted with features as columns and samples as rows.
- The transpose of this format is also okay.
- Possible features in this file include taxonomy or genes.
- Metadata file
- This file is tab-delimited.
- Formatted with features as columns and samples as rows.
- The transpose of this format is also okay.
- Possible metadata in this file include gender or age.
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.
Output Files
MaAsLin2 generates two types of output files: data and visualization.
- Data output files
all_results.tsv- This includes the same data as the data.frame returned.
- This file contains all results ordered by increasing q-value.
- The first columns are the metadata and feature names.
- The next two columns are the value and coefficient from the model.
- The next column is the standard deviation from the model.
- The
Ncolumn is the total number of data points. - The
N.not.zerocolumn is the total of non-zero data points. - The pvalue from the calculation is the second to last column.
- The qvalue is computed with
p.adjustwith the correction method.
significant_results.tsv- This file is a subset of the results in the first file.
- It only includes associations with q-values <= to the threshold.
residuals.rds- This file contains a data frame with residuals for each feature.
fitted.rds- This file contains a data frame with fitted values for each feature.
ranef.rds- This file contains a data frame with extracted random effects for each feature (when random effects are specified).
maaslin2.log- This file contains all log information for the run.
- It includes all settings, warnings, errors, and steps run.
- Visualization output files
heatmap.pdf- This file contains a heatmap of the significant associations.
[a-z/0-9]+.pdf- A plot is generated for each significant association.
- Scatter plots are used for continuous metadata.
- Box plots are for categorical data.
- Data points plotted are after normalization, filtering, and transform.
Run a Demo
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.
Command line
$ Maaslin2.R --transform=AST --fixed_effects="diagnosis,dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age" --random_effects="site,subject" --normalization=NONE --standardize=FALSE inst/extdata/HMP2_taxonomy.tsv inst/extdata/HMP2_metadata.tsv demo_output
- Make sure to provide the full path to the MaAsLin2 executable (ie ./R/Maaslin2.R).
- In the demo command:
HMP2_taxonomy.tsvis the path to your data (or features) fileHMP2_metadata.tsvis the path to your metadata filedemo_outputis the path to the folder to write the output
In R
library(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', transform = "AST",
fixed_effects = c('diagnosis', 'dysbiosisnonIBD','dysbiosisUC','dysbiosisCD', 'antibiotics', 'age'),
random_effects = c('site', 'subject'),
reference = "diagnosis,nonIBD",
normalization = 'NONE',
standardize = FALSE)## [1] "Creating output folder"
## [1] "Creating output figures folder"
## 2022-11-01 18:16:35.62288 INFO::Writing function arguments to log file
## 2022-11-01 18:16:35.657575 INFO::Verifying options selected are valid
## 2022-11-01 18:16:35.693143 INFO::Determining format of input files
## 2022-11-01 18:16:35.694362 INFO::Input format is data samples as rows and metadata samples as rows
## 2022-11-01 18:16:35.698655 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
## 2022-11-01 18:16:35.699767 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
## 2022-11-01 18:16:35.701829 INFO::Filter data based on min abundance and min prevalence
## 2022-11-01 18:16:35.702496 INFO::Total samples in data: 1595
## 2022-11-01 18:16:35.703121 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
## 2022-11-01 18:16:35.708089 INFO::Total filtered features: 0
## 2022-11-01 18:16:35.708958 INFO::Filtered feature names from abundance and prevalence filtering:
## 2022-11-01 18:16:35.71749 INFO::Total filtered features with variance filtering: 0
## 2022-11-01 18:16:35.718359 INFO::Filtered feature names from variance filtering:
## 2022-11-01 18:16:35.719015 INFO::Running selected normalization method: NONE
## 2022-11-01 18:16:35.719705 INFO::Bypass z-score application to metadata
## 2022-11-01 18:16:35.720313 INFO::Running selected transform method: AST
## 2022-11-01 18:16:35.73494 INFO::Running selected analysis method: LM
## 2022-11-01 18:16:37.444424 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:37.806954 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
## 2022-11-01 18:16:37.974616 INFO::Fitting model to feature number 3, Bifidobacterium.longum## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:38.136678 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:38.279056 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
## 2022-11-01 18:16:38.423048 INFO::Fitting model to feature number 6, Bacteroides.caccae## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:38.586953 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
## 2022-11-01 18:16:38.724997 INFO::Fitting model to feature number 8, Bacteroides.dorei## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:38.863701 INFO::Fitting model to feature number 9, Bacteroides.eggerthii## boundary (singular) fit: see help('isSingular')## Warning: Model failed to converge with 1 negative eigenvalue: -5.6e+00## 2022-11-01 18:16:39.010446 INFO::Fitting model to feature number 10, Bacteroides.faecis
## 2022-11-01 18:16:39.162157 INFO::Fitting model to feature number 11, Bacteroides.finegoldii## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:39.303681 INFO::Fitting model to feature number 12, Bacteroides.fragilis## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:39.446796 INFO::Fitting model to feature number 13, Bacteroides.intestinalis## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:39.594193 INFO::Fitting model to feature number 14, Bacteroides.massiliensis## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:39.741891 INFO::Fitting model to feature number 15, Bacteroides.ovatus
## 2022-11-01 18:16:39.886081 INFO::Fitting model to feature number 16, Bacteroides.salyersiae## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:40.026212 INFO::Fitting model to feature number 17, Bacteroides.stercoris
## 2022-11-01 18:16:40.181802 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:40.345487 INFO::Fitting model to feature number 19, Bacteroides.uniformis## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:40.489698 INFO::Fitting model to feature number 20, Bacteroides.vulgatus## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:40.665312 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:40.822679 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
## 2022-11-01 18:16:40.964734 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
## 2022-11-01 18:16:41.107285 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
## 2022-11-01 18:16:41.255893 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:41.398753 INFO::Fitting model to feature number 26, Parabacteroides.distasonis## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:41.552598 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
## 2022-11-01 18:16:41.702626 INFO::Fitting model to feature number 28, Parabacteroides.merdae
## 2022-11-01 18:16:41.84671 INFO::Fitting model to feature number 29, Parabacteroides.unclassified## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:42.002893 INFO::Fitting model to feature number 30, Paraprevotella.clara
## 2022-11-01 18:16:42.142473 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
## 2022-11-01 18:16:42.288601 INFO::Fitting model to feature number 32, Prevotella.copri## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:42.436813 INFO::Fitting model to feature number 33, Alistipes.finegoldii## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:42.587115 INFO::Fitting model to feature number 34, Alistipes.onderdonkii## boundary (singular) fit: see help('isSingular')## Warning: Model failed to converge with 1 negative eigenvalue: -1.1e+01## 2022-11-01 18:16:42.740816 INFO::Fitting model to feature number 35, Alistipes.putredinis## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:42.886245 INFO::Fitting model to feature number 36, Alistipes.shahii## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:43.023908 INFO::Fitting model to feature number 37, Alistipes.unclassified
## 2022-11-01 18:16:43.172792 INFO::Fitting model to feature number 38, Streptococcus.salivarius
## 2022-11-01 18:16:43.31387 INFO::Fitting model to feature number 39, Clostridium.bolteae## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:43.463937 INFO::Fitting model to feature number 40, Clostridium.citroniae## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:43.606369 INFO::Fitting model to feature number 41, Clostridium.clostridioforme## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:43.747633 INFO::Fitting model to feature number 42, Clostridium.hathewayi## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:43.9061 INFO::Fitting model to feature number 43, Clostridium.leptum
## 2022-11-01 18:16:44.049996 INFO::Fitting model to feature number 44, Clostridium.nexile
## 2022-11-01 18:16:44.196699 INFO::Fitting model to feature number 45, Clostridium.symbiosum## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:44.338256 INFO::Fitting model to feature number 46, Flavonifractor.plautii## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:44.478782 INFO::Fitting model to feature number 47, Eubacterium.eligens
## 2022-11-01 18:16:44.623994 INFO::Fitting model to feature number 48, Eubacterium.hallii
## 2022-11-01 18:16:44.77215 INFO::Fitting model to feature number 49, Eubacterium.rectale
## 2022-11-01 18:16:44.917501 INFO::Fitting model to feature number 50, Eubacterium.siraeum## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:45.084676 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:45.244283 INFO::Fitting model to feature number 52, Eubacterium.ventriosum## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:45.406904 INFO::Fitting model to feature number 53, Ruminococcus.gnavus## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:45.559628 INFO::Fitting model to feature number 54, Ruminococcus.obeum## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:45.706611 INFO::Fitting model to feature number 55, Ruminococcus.torques
## 2022-11-01 18:16:45.854852 INFO::Fitting model to feature number 56, Coprococcus.comes
## 2022-11-01 18:16:46.001438 INFO::Fitting model to feature number 57, Dorea.longicatena
## 2022-11-01 18:16:46.144773 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:46.31531 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:46.457723 INFO::Fitting model to feature number 60, Roseburia.hominis## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:46.60064 INFO::Fitting model to feature number 61, Roseburia.intestinalis
## 2022-11-01 18:16:46.964629 INFO::Fitting model to feature number 62, Roseburia.inulinivorans## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:47.115546 INFO::Fitting model to feature number 63, Roseburia.unclassified## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:47.258795 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
## 2022-11-01 18:16:47.408674 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:47.544792 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
## 2022-11-01 18:16:47.688243 INFO::Fitting model to feature number 67, Ruminococcus.bromii## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:47.830331 INFO::Fitting model to feature number 68, Ruminococcus.callidus
## 2022-11-01 18:16:47.982678 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
## 2022-11-01 18:16:48.137139 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
## 2022-11-01 18:16:48.281712 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
## 2022-11-01 18:16:48.428797 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.00291214 (tol = 0.002, component 1)## 2022-11-01 18:16:48.561661 INFO::Fitting model to feature number 73, Dialister.invisus## boundary (singular) fit: see help('isSingular')## Warning: Model failed to converge with 1 negative eigenvalue: -2.1e+02## 2022-11-01 18:16:48.697691 INFO::Fitting model to feature number 74, Veillonella.atypica## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:48.849149 INFO::Fitting model to feature number 75, Veillonella.dispar## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:48.991864 INFO::Fitting model to feature number 76, Veillonella.parvula## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:49.134112 INFO::Fitting model to feature number 77, Veillonella.unclassified
## 2022-11-01 18:16:49.283294 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
## 2022-11-01 18:16:49.428357 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:49.584554 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
## 2022-11-01 18:16:49.740765 INFO::Fitting model to feature number 81, Bilophila.unclassified
## 2022-11-01 18:16:49.889395 INFO::Fitting model to feature number 82, Escherichia.coli## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:50.036596 INFO::Fitting model to feature number 83, Escherichia.unclassified
## 2022-11-01 18:16:50.174981 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:50.318806 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae## boundary (singular) fit: see help('isSingular')## 2022-11-01 18:16:50.466953 INFO::Fitting model to feature number 86, Akkermansia.muciniphila## boundary (singular) fit: see help('isSingular')## Warning: Model failed to converge with 1 negative eigenvalue: -2.2e+02## 2022-11-01 18:16:50.611181 INFO::Fitting model to feature number 87, C2likevirus.unclassified
## 2022-11-01 18:16:50.798012 INFO::Counting total values for each feature
## 2022-11-01 18:16:50.828629 INFO::Writing residuals to file demo_output/residuals.rds
## 2022-11-01 18:16:50.884153 INFO::Writing fitted values to file demo_output/fitted.rds
## 2022-11-01 18:16:50.914598 INFO::Writing extracted random effects to file demo_output/ranef.rds
## 2022-11-01 18:16:50.919923 INFO::Writing all results to file (ordered by increasing q-values): demo_output/all_results.tsv
## 2022-11-01 18:16:50.926668 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
## 2022-11-01 18:16:50.929321 INFO::Writing heatmap of significant results to file: demo_output/heatmap.pdf## Warning in xtfrm.data.frame(x): cannot xtfrm data frames## 2022-11-01 18:16:51.219354 INFO::Writing association plots (one for each significant association) to output folder: demo_output
## 2022-11-01 18:16:51.226799 INFO::Plotting associations from most to least significant, grouped by metadata
## 2022-11-01 18:16:51.227981 INFO::Plotting data for metadata number 1, dysbiosisCD
## 2022-11-01 18:16:51.229525 INFO::Creating boxplot for categorical data, dysbiosisCD vs Faecalibacterium.prausnitzii## 2022-11-01 18:16:51.520358 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.uniformis## 2022-11-01 18:16:51.737648 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.rectale## 2022-11-01 18:16:51.946662 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.putredinis## 2022-11-01 18:16:52.165536 INFO::Creating boxplot for categorical data, dysbiosisCD vs Subdoligranulum.unclassified## 2022-11-01 18:16:52.367893 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.coli## 2022-11-01 18:16:52.589988 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.vulgatus## 2022-11-01 18:16:52.792596 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.clostridioforme## 2022-11-01 18:16:53.012173 INFO::Creating boxplot for categorical data, dysbiosisCD vs Klebsiella.pneumoniae## 2022-11-01 18:16:53.208281 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.hathewayi## 2022-11-01 18:16:53.420903 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.shahii## 2022-11-01 18:16:53.619987 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.obeum## 2022-11-01 18:16:53.859989 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.inulinivorans## 2022-11-01 18:16:54.067932 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.thetaiotaomicron## 2022-11-01 18:16:54.290472 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprococcus.comes## 2022-11-01 18:16:54.497377 INFO::Creating boxplot for categorical data, dysbiosisCD vs Veillonella.unclassified## 2022-11-01 18:16:54.73575 INFO::Creating boxplot for categorical data, dysbiosisCD vs Lachnospiraceae.bacterium.3.1.46FAA## 2022-11-01 18:16:54.947011 INFO::Creating boxplot for categorical data, dysbiosisCD vs Sutterella.wadsworthensis## 2022-11-01 18:16:55.169982 INFO::Creating boxplot for categorical data, dysbiosisCD vs Odoribacter.splanchnicus## 2022-11-01 18:16:55.370189 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.distasonis## 2022-11-01 18:16:55.583633 INFO::Creating boxplot for categorical data, dysbiosisCD vs Roseburia.hominis## 2022-11-01 18:16:55.787652 INFO::Creating boxplot for categorical data, dysbiosisCD vs Burkholderiales.bacterium.1.1.47## 2022-11-01 18:16:56.003016 INFO::Creating boxplot for categorical data, dysbiosisCD vs Escherichia.unclassified## 2022-11-01 18:16:56.2084 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bilophila.unclassified## 2022-11-01 18:16:56.451123 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dorea.longicatena## 2022-11-01 18:16:56.656787 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.unclassified## 2022-11-01 18:16:56.882359 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.symbiosum## 2022-11-01 18:16:57.081513 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.hallii## 2022-11-01 18:16:57.305144 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parasutterella.excrementihominis## 2022-11-01 18:16:57.510079 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.stercoris## 2022-11-01 18:16:57.728 INFO::Creating boxplot for categorical data, dysbiosisCD vs Alistipes.finegoldii## 2022-11-01 18:16:57.940423 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.ventriosum## 2022-11-01 18:16:58.166943 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.nexile## 2022-11-01 18:16:58.367079 INFO::Creating boxplot for categorical data, dysbiosisCD vs Clostridium.leptum## 2022-11-01 18:16:58.57933 INFO::Creating boxplot for categorical data, dysbiosisCD vs Veillonella.parvula## 2022-11-01 18:16:58.779856 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.ovatus## 2022-11-01 18:16:59.006413 INFO::Creating boxplot for categorical data, dysbiosisCD vs Oscillibacter.unclassified## 2022-11-01 18:16:59.239188 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.finegoldii## 2022-11-01 18:16:59.471393 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.bromii## 2022-11-01 18:16:59.668582 INFO::Creating boxplot for categorical data, dysbiosisCD vs Coprobacillus.unclassified## 2022-11-01 18:16:59.883466 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.merdae## 2022-11-01 18:17:00.083689 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.eggerthii## 2022-11-01 18:17:00.304032 INFO::Creating boxplot for categorical data, dysbiosisCD vs Veillonella.dispar## 2022-11-01 18:17:00.506679 INFO::Creating boxplot for categorical data, dysbiosisCD vs Collinsella.aerofaciens## 2022-11-01 18:17:00.73386 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.caccae## 2022-11-01 18:17:00.944498 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.gnavus## 2022-11-01 18:17:01.172177 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.clara## 2022-11-01 18:17:01.393354 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.xylanisolvens## 2022-11-01 18:17:01.593033 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.lactaris## 2022-11-01 18:17:01.817166 INFO::Creating boxplot for categorical data, dysbiosisCD vs Paraprevotella.unclassified## 2022-11-01 18:17:02.025422 INFO::Creating boxplot for categorical data, dysbiosisCD vs Ruminococcus.torques## 2022-11-01 18:17:02.238057 INFO::Creating boxplot for categorical data, dysbiosisCD vs C2likevirus.unclassified## 2022-11-01 18:17:02.449535 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bacteroides.faecis## 2022-11-01 18:17:02.657531 INFO::Creating boxplot for categorical data, dysbiosisCD vs Bifidobacterium.longum## 2022-11-01 18:17:02.871721 INFO::Creating boxplot for categorical data, dysbiosisCD vs Eubacterium.siraeum## 2022-11-01 18:17:03.084774 INFO::Creating boxplot for categorical data, dysbiosisCD vs Dialister.invisus## 2022-11-01 18:17:03.370263 INFO::Creating boxplot for categorical data, dysbiosisCD vs Parabacteroides.unclassified## 2022-11-01 18:17:06.235441 INFO::Plotting data for metadata number 2, dysbiosisUC
## 2022-11-01 18:17:06.237346 INFO::Creating boxplot for categorical data, dysbiosisUC vs Subdoligranulum.unclassified## 2022-11-01 18:17:06.416158 INFO::Creating boxplot for categorical data, dysbiosisUC vs Prevotella.copri## 2022-11-01 18:17:06.639788 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.fragilis## 2022-11-01 18:17:06.83999 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.caccae## 2022-11-01 18:17:07.059313 INFO::Creating boxplot for categorical data, dysbiosisUC vs Faecalibacterium.prausnitzii## 2022-11-01 18:17:07.273318 INFO::Creating boxplot for categorical data, dysbiosisUC vs Oscillibacter.unclassified## 2022-11-01 18:17:07.495466 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.uniformis## 2022-11-01 18:17:07.704334 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.hallii## 2022-11-01 18:17:07.927812 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.faecis## 2022-11-01 18:17:08.133892 INFO::Creating boxplot for categorical data, dysbiosisUC vs Klebsiella.pneumoniae## 2022-11-01 18:17:08.347777 INFO::Creating boxplot for categorical data, dysbiosisUC vs Coprobacillus.unclassified## 2022-11-01 18:17:08.543893 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.stercoris## 2022-11-01 18:17:08.759754 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.rectale## 2022-11-01 18:17:08.968373 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.gnavus## 2022-11-01 18:17:09.216121 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.ovatus## 2022-11-01 18:17:09.441144 INFO::Creating boxplot for categorical data, dysbiosisUC vs Lachnospiraceae.bacterium.3.1.46FAA## 2022-11-01 18:17:09.677791 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.siraeum## 2022-11-01 18:17:09.887759 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.putredinis## 2022-11-01 18:17:10.109864 INFO::Creating boxplot for categorical data, dysbiosisUC vs Ruminococcus.obeum## 2022-11-01 18:17:10.318163 INFO::Creating boxplot for categorical data, dysbiosisUC vs Escherichia.coli## 2022-11-01 18:17:10.548195 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.eggerthii## 2022-11-01 18:17:10.757798 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.leptum## 2022-11-01 18:17:10.97863 INFO::Creating boxplot for categorical data, dysbiosisUC vs Barnesiella.intestinihominis## 2022-11-01 18:17:11.212588 INFO::Creating boxplot for categorical data, dysbiosisUC vs Alistipes.shahii## 2022-11-01 18:17:11.426229 INFO::Creating boxplot for categorical data, dysbiosisUC vs Collinsella.aerofaciens## 2022-11-01 18:17:11.662742 INFO::Creating boxplot for categorical data, dysbiosisUC vs Clostridium.nexile## 2022-11-01 18:17:11.877998 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bacteroides.xylanisolvens## 2022-11-01 18:17:12.101785 INFO::Creating boxplot for categorical data, dysbiosisUC vs Parabacteroides.goldsteinii## 2022-11-01 18:17:12.312061 INFO::Creating boxplot for categorical data, dysbiosisUC vs Eubacterium.ventriosum## 2022-11-01 18:17:12.532078 INFO::Creating boxplot for categorical data, dysbiosisUC vs Coprococcus.comes## 2022-11-01 18:17:12.747787 INFO::Creating boxplot for categorical data, dysbiosisUC vs Bifidobacterium.adolescentis## 2022-11-01 18:17:12.950923 INFO::Creating boxplot for categorical data, dysbiosisUC vs Veillonella.atypica## 2022-11-01 18:17:15.811393 INFO::Plotting data for metadata number 3, dysbiosisnonIBD
## 2022-11-01 18:17:15.813171 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Faecalibacterium.prausnitzii## 2022-11-01 18:17:16.246954 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.rectale## 2022-11-01 18:17:16.450186 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Prevotella.copri## 2022-11-01 18:17:16.660842 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.sp.3.1.31## 2022-11-01 18:17:16.850961 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Roseburia.hominis## 2022-11-01 18:17:17.051153 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Odoribacter.splanchnicus## 2022-11-01 18:17:17.253333 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bilophila.unclassified## 2022-11-01 18:17:17.459432 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Escherichia.coli## 2022-11-01 18:17:17.663135 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Subdoligranulum.unclassified## 2022-11-01 18:17:17.872729 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.leptum## 2022-11-01 18:17:18.084618 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.fragilis## 2022-11-01 18:17:18.288522 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Klebsiella.pneumoniae## 2022-11-01 18:17:18.484631 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.torques## 2022-11-01 18:17:18.680702 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Clostridium.clostridioforme## 2022-11-01 18:17:18.88748 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.putredinis## 2022-11-01 18:17:19.087026 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Coprobacillus.unclassified## 2022-11-01 18:17:19.283914 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Eubacterium.eligens## 2022-11-01 18:17:19.486838 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Veillonella.dispar## 2022-11-01 18:17:19.687378 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Bacteroides.eggerthii## 2022-11-01 18:17:19.894331 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Lachnospiraceae.bacterium.3.1.46FAA## 2022-11-01 18:17:20.095945 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.obeum## 2022-11-01 18:17:20.306382 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Ruminococcus.bromii## 2022-11-01 18:17:20.510443 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Parasutterella.excrementihominis## 2022-11-01 18:17:20.712313 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Alistipes.shahii## 2022-11-01 18:17:20.921217 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Barnesiella.intestinihominis## 2022-11-01 18:17:21.119638 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Burkholderiales.bacterium.1.1.47## 2022-11-01 18:17:21.323332 INFO::Creating boxplot for categorical data, dysbiosisnonIBD vs Paraprevotella.unclassified## 2022-11-01 18:17:24.037088 INFO::Plotting data for metadata number 4, antibiotics
## 2022-11-01 18:17:24.038949 INFO::Creating boxplot for categorical data, antibiotics vs Escherichia.coli## 2022-11-01 18:17:24.209781 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.inulinivorans## 2022-11-01 18:17:24.402878 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.intestinalis## 2022-11-01 18:17:24.60401 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroidales.bacterium.ph8## 2022-11-01 18:17:24.857917 INFO::Creating boxplot for categorical data, antibiotics vs Roseburia.hominis## 2022-11-01 18:17:25.052901 INFO::Creating boxplot for categorical data, antibiotics vs Dialister.invisus## 2022-11-01 18:17:25.251045 INFO::Creating boxplot for categorical data, antibiotics vs Klebsiella.pneumoniae## 2022-11-01 18:17:25.455293 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.rectale## 2022-11-01 18:17:25.645374 INFO::Creating boxplot for categorical data, antibiotics vs Sutterella.wadsworthensis## 2022-11-01 18:17:25.856248 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.thetaiotaomicron## 2022-11-01 18:17:26.047179 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.callidus## 2022-11-01 18:17:26.258385 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.finegoldii## 2022-11-01 18:17:26.444862 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.onderdonkii## 2022-11-01 18:17:26.643457 INFO::Creating boxplot for categorical data, antibiotics vs Dorea.longicatena## 2022-11-01 18:17:26.838602 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.pseudocatenulatum## 2022-11-01 18:17:27.044663 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.longum## 2022-11-01 18:17:27.231242 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.bolteae## 2022-11-01 18:17:27.436265 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.hathewayi## 2022-11-01 18:17:27.64312 INFO::Creating boxplot for categorical data, antibiotics vs Faecalibacterium.prausnitzii## 2022-11-01 18:17:27.849113 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.bromii## 2022-11-01 18:17:28.048868 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.eligens## 2022-11-01 18:17:28.247867 INFO::Creating boxplot for categorical data, antibiotics vs Ruminococcus.obeum## 2022-11-01 18:17:28.441147 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.fragilis## 2022-11-01 18:17:28.650762 INFO::Creating boxplot for categorical data, antibiotics vs Escherichia.unclassified## 2022-11-01 18:17:28.858891 INFO::Creating boxplot for categorical data, antibiotics vs Bilophila.unclassified## 2022-11-01 18:17:29.067544 INFO::Creating boxplot for categorical data, antibiotics vs Eubacterium.sp.3.1.31## 2022-11-01 18:17:29.260641 INFO::Creating boxplot for categorical data, antibiotics vs Alistipes.putredinis## 2022-11-01 18:17:29.456615 INFO::Creating boxplot for categorical data, antibiotics vs Veillonella.parvula## 2022-11-01 18:17:29.650651 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.caccae## 2022-11-01 18:17:29.860832 INFO::Creating boxplot for categorical data, antibiotics vs Parabacteroides.distasonis## 2022-11-01 18:17:30.060359 INFO::Creating boxplot for categorical data, antibiotics vs Parabacteroides.merdae## 2022-11-01 18:17:30.267694 INFO::Creating boxplot for categorical data, antibiotics vs Parasutterella.excrementihominis## 2022-11-01 18:17:30.462391 INFO::Creating boxplot for categorical data, antibiotics vs Bifidobacterium.adolescentis## 2022-11-01 18:17:30.663749 INFO::Creating boxplot for categorical data, antibiotics vs Lachnospiraceae.bacterium.1.1.57FAA## 2022-11-01 18:17:30.853581 INFO::Creating boxplot for categorical data, antibiotics vs Akkermansia.muciniphila## 2022-11-01 18:17:31.057609 INFO::Creating boxplot for categorical data, antibiotics vs Clostridium.symbiosum## 2022-11-01 18:17:31.251166 INFO::Creating boxplot for categorical data, antibiotics vs Paraprevotella.clara## 2022-11-01 18:17:31.463266 INFO::Creating boxplot for categorical data, antibiotics vs Bacteroides.faecis## 2022-11-01 18:17:34.12964 INFO::Plotting data for metadata number 5, age
## 2022-11-01 18:17:34.13173 INFO::Creating scatter plot for continuous data, age vs Clostridium.clostridioforme## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:34.354636 INFO::Creating scatter plot for continuous data, age vs Haemophilus.parainfluenzae## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:34.628431 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.pseudocatenulatum## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:34.820309 INFO::Creating scatter plot for continuous data, age vs Subdoligranulum.unclassified## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:35.029851 INFO::Creating scatter plot for continuous data, age vs Bacteroides.intestinalis## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:35.23652 INFO::Creating scatter plot for continuous data, age vs Faecalibacterium.prausnitzii## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:35.440342 INFO::Creating scatter plot for continuous data, age vs Clostridium.symbiosum## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:35.66076 INFO::Creating scatter plot for continuous data, age vs Ruminococcus.bromii## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:35.852525 INFO::Creating scatter plot for continuous data, age vs Akkermansia.muciniphila## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:36.06627 INFO::Creating scatter plot for continuous data, age vs Veillonella.dispar## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:36.272758 INFO::Creating scatter plot for continuous data, age vs Collinsella.aerofaciens## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:36.484215 INFO::Creating scatter plot for continuous data, age vs Roseburia.intestinalis## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:36.680741 INFO::Creating scatter plot for continuous data, age vs Bacteroides.thetaiotaomicron## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:36.893986 INFO::Creating scatter plot for continuous data, age vs Dialister.invisus## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:37.113481 INFO::Creating scatter plot for continuous data, age vs Acidaminococcus.unclassified## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:37.310317 INFO::Creating scatter plot for continuous data, age vs Veillonella.unclassified## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:37.521023 INFO::Creating scatter plot for continuous data, age vs Bifidobacterium.longum## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:37.740067 INFO::Creating scatter plot for continuous data, age vs Alistipes.unclassified## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:37.976754 INFO::Creating scatter plot for continuous data, age vs Bacteroidales.bacterium.ph8## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## `geom_smooth()` using formula 'y ~ x'## Warning: Removed 19 rows containing missing values (geom_point).## 2022-11-01 18:17:40.790729 INFO::Plotting data for metadata number 6, diagnosis
## 2022-11-01 18:17:40.792622 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.clostridioforme## 2022-11-01 18:17:40.991468 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.bolteae## 2022-11-01 18:17:41.213503 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.putredinis## 2022-11-01 18:17:41.433563 INFO::Creating boxplot for categorical data, diagnosis vs Oscillibacter.unclassified## 2022-11-01 18:17:41.660703 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.shahii## 2022-11-01 18:17:41.874889 INFO::Creating boxplot for categorical data, diagnosis vs Collinsella.aerofaciens## 2022-11-01 18:17:42.176527 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila## 2022-11-01 18:17:42.390059 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified## 2022-11-01 18:17:42.613051 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.goldsteinii## 2022-11-01 18:17:42.817383 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii## 2022-11-01 18:17:43.039623 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.callidus## 2022-11-01 18:17:43.253067 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis## 2022-11-01 18:17:43.487525 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.bromii## 2022-11-01 18:17:43.704592 INFO::Creating boxplot for categorical data, diagnosis vs Akkermansia.muciniphila## 2022-11-01 18:17:43.918393 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.obeum## 2022-11-01 18:17:44.136621 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroidales.bacterium.ph8## 2022-11-01 18:17:44.349942 INFO::Creating boxplot for categorical data, diagnosis vs Bifidobacterium.adolescentis## 2022-11-01 18:17:44.569082 INFO::Creating boxplot for categorical data, diagnosis vs Bacteroides.fragilis## 2022-11-01 18:17:44.774282 INFO::Creating boxplot for categorical data, diagnosis vs Alistipes.finegoldii## 2022-11-01 18:17:44.995952 INFO::Creating boxplot for categorical data, diagnosis vs Clostridium.leptum## 2022-11-01 18:17:45.198872 INFO::Creating boxplot for categorical data, diagnosis vs Sutterella.wadsworthensis## 2022-11-01 18:17:45.417676 INFO::Creating boxplot for categorical data, diagnosis vs Escherichia.unclassified## 2022-11-01 18:17:45.619402 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.lactaris## 2022-11-01 18:17:45.844759 INFO::Creating boxplot for categorical data, diagnosis vs Bilophila.unclassified## 2022-11-01 18:17:46.059859 INFO::Creating boxplot for categorical data, diagnosis vs Ruminococcus.gnavus## 2022-11-01 18:17:46.26833 INFO::Creating boxplot for categorical data, diagnosis vs Subdoligranulum.unclassified## 2022-11-01 18:17:46.490336 INFO::Creating boxplot for categorical data, diagnosis vs Coprobacillus.unclassified## 2022-11-01 18:17:46.720839 INFO::Creating boxplot for categorical data, diagnosis vs Parabacteroides.unclassified
Session Info
Session info from running the demo in R can be displayed with the following command.
sessionInfo()## R Under development (unstable) (2022-10-25 r83175)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.17-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
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] Maaslin2_1.13.0
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.1 biglm_0.9-2.1 xfun_0.34
## [4] bslib_0.4.0 ggplot2_3.3.6 lattice_0.20-45
## [7] numDeriv_2016.8-1.1 vctrs_0.5.0 tools_4.3.0
## [10] generics_0.1.3 parallel_4.3.0 getopt_1.20.3
## [13] tibble_3.1.8 fansi_1.0.3 highr_0.9
## [16] DEoptimR_1.0-11 pkgconfig_2.0.3 logging_0.10-108
## [19] pheatmap_1.0.12 Matrix_1.5-1 data.table_1.14.4
## [22] RColorBrewer_1.1-3 assertthat_0.2.1 lifecycle_1.0.3
## [25] lpsymphony_1.27.0 farver_2.1.1 compiler_4.3.0
## [28] stringr_1.4.1 munsell_0.5.0 lmerTest_3.1-3
## [31] htmltools_0.5.3 sass_0.4.2 hash_2.2.6.2
## [34] yaml_2.3.6 pillar_1.8.1 nloptr_2.0.3
## [37] crayon_1.5.2 jquerylib_0.1.4 MASS_7.3-58.1
## [40] cachem_1.0.6 boot_1.3-28 nlme_3.1-160
## [43] robustbase_0.95-0 tidyselect_1.2.0 digest_0.6.30
## [46] mvtnorm_1.1-3 stringi_1.7.8 dplyr_1.0.10
## [49] labeling_0.4.2 splines_4.3.0 pcaPP_2.0-3
## [52] fastmap_1.1.0 grid_4.3.0 colorspace_2.0-3
## [55] cli_3.4.1 magrittr_2.0.3 utf8_1.2.2
## [58] withr_2.5.0 scales_1.2.1 rmarkdown_2.17
## [61] lme4_1.1-31 pbapply_1.5-0 evaluate_0.17
## [64] knitr_1.40 mgcv_1.8-41 rlang_1.0.6
## [67] Rcpp_1.0.9 glue_1.6.2 optparse_1.7.3
## [70] DBI_1.1.3 minqa_1.2.5 jsonlite_1.8.3
## [73] R6_2.5.1Options
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 ]
-e CORES, --cores=CORES
The number of R processes to run in parallel
[ Default: 1 ]
-d REFERENCE, --reference=REFERENCE
The factor to use as a reference for a variable
with more than two levels provided as a string
of 'variable,reference' semi-colon delimited
for multiple variables [ Default: NA ] Troubleshooting
- Question: When I run from the command line I see the error
Maaslin2.R: command not found. How do I fix this?- Answer: Provide the full path to the executable when running Maaslin2.R.
- Question: When I run as a function I see the error
Error in library(Maaslin2): there is no package called 'Maaslin2'. How do I fix this?- Answer: Install the R package and then try loading the library again.
- Question: When I try to install the R package I see errors about dependencies not being installed. Why is this?
- Answer: Installing the R package will not automatically install the packages MaAsLin2 requires. Please install the dependencies and then install the MaAsLin2 R package.