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bngal command details
Matt Selensky edited this page May 23, 2024
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IMPORTANT NOTE: The bngal documentation has moved and these Wiki pages are no longer maintained! Please visit https://mselensky.github.io/bngal/commands/ for the most up-to-date documentation.
Run bngal-build-nets --help for details:
Usage: bngal-build-nets [options]
Options:
-a ASV_TABLE, --asv_table=ASV_TABLE
(Required) Taxonomic count table named by Silva- or GTDB-style taxonomies
(i.e., d__DOMAIN;p__PHYLUM;c__CLASS;o__ORDER;f__FAMILY;g__GENUS;s__SPECIES). Ideally rarefied and filtered as necessary.
* First column must be named 'sample-id' and must contain unique identifiers.
* Must be an absolute abundance table.
* If the input table is collapsed higher than level 7 (ASV/OTU), be sure to specify the --taxonomic_level option accordingly.
-m METADATA, --metadata=METADATA
(Required) Sample metadata corresponding to asv_table. Must be a .CSV file with sample identifiers in a column named `sample-id.`
-o OUTPUT, --output=OUTPUT
Output directory for network graphs and data.
* Default = bngal-results
-c CORRELATION, --correlation=CORRELATION
Metric for pairwise comparisons. Can be one of 'pearson' or 'spearman'.
* Default = spearman
-l TRANSFORMATION, --transformation=TRANSFORMATION
Numeric transformation to apply to input data before correlation calculations.
Can be one of 'log10'.
* Default = NULL
-r CORR_COLUMNS, --corr_columns=CORR_COLUMNS
Metadata columns to include in pairwise correlation networks.
* Multiple columns may be provided given the following syntax: 'col1,col2'
* Default = NULL
-k CORR_CUTOFF, --corr_cutoff=CORR_CUTOFF
Absolute correlation coefficient cutoff for pairwise comparisons.
* Default = 0.6
-p P_VALUE, --p_value=P_VALUE
Maximum cutoff for p-values calculated from pairwise relationships.
* Default = 0.05
-f ABUN_CUTOFF, --abun_cutoff=ABUN_CUTOFF
Relative abundance cutoff for taxa (values 0-1 accepted). Anything lower than this value is removed before network construction.
* Default = 0
-x CORES, --cores=CORES
Number of CPUs to use. Can only parallelize on Mac or Linux OS.
* Default = 1
-n SUBNETWORKS, --subnetworks=SUBNETWORKS
Metadata column by which to split data in order to create separate networks.
* If not provided, bngal will create a single network from the input ASV table.
* Default = NULL
-t TAXONOMIC_LEVEL, --taxonomic_level=TAXONOMIC_LEVEL
Taxonomic level at which to construct co-occurrence networks. Must be at the same level or above the input --asv_table.
Can be one of 'phylum', 'class', 'order', 'family', 'genus', or 'asv'
* Default = asv
-d DIRECTION, --direction=DIRECTION
Direction for --abun-cutoff. Can be one of 'greaterThan' or 'lessThan'.
* Default = 'greaterThan'
-s SIGN, --sign=SIGN
Type of pairwise relationship for network construction. Can be one of 'positive', 'negative', or 'all'.
* Default = 'all'
-b OBS_THRESHOLD, --obs_threshold=OBS_THRESHOLD
('Observational threshold') Minimum number of unique observations required for a given pairwise relationship to be included in the network.
* Default = 5
-g GRAPH_LAYOUT, --graph_layout=GRAPH_LAYOUT
Type of igraph layout for output network plots.
* Refer to the igraph documentation for the full list of options:
https://igraph.org/r/html/latest/layout_.html
* Default = 'layout_nicely'
-h, --help
Show this help message and exit
Run bngal-summarize-nets --help for more details:
Usage: bngal-summarize-nets [options]
Options:
-a ASV_TABLE, --asv_table=ASV_TABLE
(Required) Taxonomic count table named by Silva- or GTDB-style taxonomies
(i.e., d__DOMAIN;p__PHYLUM;c__CLASS;o__ORDER;f__FAMILY;g__GENUS;s__SPECIES). Ideally rarefied and filtered as necessary.
* First column must be named 'sample-id' and must contain unique identifiers.
* Must be an absolute abundance table.
* If the input table is collapsed higher than level 7 (ASV/OTU), be sure to specify the --taxonomic_level option accordingly.
-m METADATA, --metadata=METADATA
(Required) Sample metadata corresponding to asv_table. Must be a .CSV file with sample identifiers in a column named `sample-id.`
-w NETWORK_DIR, --network_dir=NETWORK_DIR
(Required) Input network data. Should be parent folder of `bngal-build-nets` output. Output subfolders will write here as well unless --output is specified.
-o OUTPUT, --output=OUTPUT
Optional output folder. May be useful if one desires to test multiple `-f` inputs on the same network data.
-t TAXONOMIC_LEVEL, --taxonomic_level=TAXONOMIC_LEVEL
Taxonomic level at which to construct co-occurrence networks. Must be at the same level or above the input --asv_table.
Can be one of 'phylum', 'class', 'order', 'family', 'genus', or 'asv'
* Default = asv
-n SUBNETWORKS, --subnetworks=SUBNETWORKS
Metadata column by which to split data in order to create separate networks.
* If not provided, bngal will create a single network from the input ASV table.
* Default = NULL
-f FILL_EBC_BY, --fill_ebc_by=FILL_EBC_BY
Metadata column by which to fill EBC composition plots.
* Default = NULL
-i INTERACTIVE, --interactive=INTERACTIVE
Determines whether output EBC composition plots are exported as interactive HTMLs (TRUE) or static PDFs (FALSE)
* Default = FALSE
-x CORES, --cores=CORES
Number of CPUs to use. Can only parallelize on Mac or Linux OS. Currently, bngal can only run on multiple cores when --subnetworks is provided.
* Default = 1
-q QUERY, --query=QUERY
A query string to construct co-occurrence plots for a specific taxon.
Be sure to use the full taxonomic ID as appropriate for the given taxonomic level as noted in the *taxa_spread.csv output in the network-summaries subfolder.
Multiple queries may be provided given space characters: 'Archaea;Crenarchaeota Bacteria;Actinobacteriota'
* Default = NULL
-s SKIP_PLOTTING, --skip_plotting=SKIP_PLOTTING
Skip the plotting of taxonomic barplots and EBC composition plots. Useful if you want to test multiple --query inputs on the same data.
* Default = FALSE
-h, --help
Show this help message and exit