Table of contents

  1. bngal-build-nets
  2. bngal-summarize-nets

bngal-build-nets

Build a network from input abundance data.

bngal-build-nets --help

--asv_table

  • (Required) Path to taxonomic count table named by Silva138-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.
    • A formatted example table can be found here (download)

--metadata

  • (Required) Sample metadata corresponding to asv_table. Must be a .CSV file with sample identifiers in a column named sample-id.
    • A formatted example table can be found here (download)

--output

  • (Optional) Output directory for networks and graphs.
    Default = ./bngal-results

--correlation

  • (Optional) Metric for pairwise comparisons. Can be one of pearson or spearman.
    Default = spearman

--transformation

  • (Optional) Numeric transformation to apply to input data before correlation calculations. Can be one of log10 or NULL.
    Default = NULL

--corr_columns

  • (Optional) Metadata columns to include in pairwise correlation networks. Multiple columns may be provided given the following syntax: 'col1,col2'.
    Default = NULL

--corr_cutoff

  • (Optional) Absolute correlation coefficient (defined from --correlation) cutoff for pairwise comparisons.
    Default = 0.6

--p_value

  • (Optional) Maximum cutoff for p-values calculated from pairwise relationships.
    Default = 0.05

--abun_cutoff

  • (Optional) Relative abundance cutoff for taxa (values 0-1 accepted). Anything lower than this value is removed before network construction.
    Default = 0

--cores

  • (Optional) Number of CPUs to use. Can only parallelize on Mac or Linux OS.
    Default = 1

--subnetworks

  • (Optional) 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

--taxonomic_level

  • (Optional) 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

--direction

  • (Optional) Direction for --abun-cutoff. Can be one of greaterThan or lessThan.
    Default = greaterThan

--sign

  • (Optional) Type of pairwise relationship to filter for network construction. Can be one of positive (--corr_cutoff > 0), negative (--corr_cutoff < 0), or all (--corr_cutoff > 0 and --corr_cutoff < 0).
    Default = all

--obs_threshold

  • (Optional) ‘Observational threshold’. Minimum number of unique observations required for a given pairwise relationship to be included in the network.
    Default = 5

--graph_layout

  • (Optional) Type of igraph layout for output network plots. Refer to the igraph documentation for the full list of options.
    Default = layout_nicely

bngal-summarize-nets

Summarize network statistics from bngal-build-nets output.

bngal-summarize-nets --help

--asv_table

--metadata

--output

--taxonomic_level

--subnetworks

--fill_ebc_by

  • (Optional) Metadata column by which to fill EBC composition plots.
    Default = NULL

--interactive

  • (Optional) Determines whether output EBC composition plots are exported as interactive HTMLs (TRUE) or static PDFs (FALSE).
    Default = FALSE

--cores

--query

  • (Optional) 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

--tip_shape_by

  • (Optional) Define the shape of the summary barplot’s dendrogram tips by a metadata column.
    Default = NULL

--skip_plotting

  • (Optional) 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