NAME¶

ktImportTaxonomy - explore hierarchical metagenomic data with zoomable pie charts

DESCRIPTION¶

Creates a Krona chart based on taxonomy IDs and, optionally, magnitudes and scores. Taxonomy IDs corresponding to a rank of "no rank" in the database will be assigned to their parents to make the hierarchy less cluttered (e.g. "Cellular organisms" will be assigned to "root").

ktImportTaxonomy \

[options] \ taxonomy_1[:magnitudes_1][,name_1] \ [taxonomy_2[:magnitudes_2][,name_2]] \ ...

taxonomy

Tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes and scores. By default, query IDs, taxonomy IDs and scores will be taken from columns 1, 2 and 3, respectively (see -q, -t, -s, and -m). Lines beginning with "#" will be ignored. By default, separate datasets will be created for each input (see [-c]).

magnitudes

Optional file listing query IDs with magnitudes, separated by tabs. This can be used to account for read length or contig depth to obtain a more accurate representation of abundance. By default, query sequences without specified magnitudes will be assigned a magnitude of 1. Magnitude files for assemblies in ACE format can be created with ktGetContigMagnitudes.

name

A name to show in the list of datasets in the Krona chart (if multiple input files are present and [-c] is not specified). By default, the basename of the file will be used.

[-o <string>]

Output file name. [Default: 'taxonomy.krona.html']

[-n <string>]

Name of the highest level. [Default: 'Root']

[-i]

Include a wedge for queries with no hits.

[-c]

Combine data from each file, rather than creating separate datasets within the chart.

[-q <integer>]

Column of input files to use as query ID. Required if magnitude files are specified. [Default: '1']

[-t <integer>]

Column of input files to use as taxonomy ID. [Default: '2']

[-s <integer>]

Column of input files to use as score. [Default: '3']

[-m <integer>]

Column of input files to use as magnitude. If magnitude files are specified, their magnitudes will override those in this column.

[-d <integer>]

Maximum depth of wedges to include in the chart.

[-k]

Show the "cellular organisms" taxon (collapsed by default).

[-K]

Collapse assignments to taxa with ranks labeled "no rank" by moving up to parent.

[-x <integer>]

Hue (0-360) for "bad" scores. [Default: '0']

[-y <integer>]

Hue (0-360) for "good" scores. [Default: '120']

[-u <string>]

URL of Krona resources to use instead of bundling them with the chart (e.g. "http://krona.sourceforge.net"). Reduces size of charts and allows updates, though charts will not work without access to this URL.

[-qp <string>]

Url to send query IDs to (instead of listing them) for each wedge. The query IDs will be sent as a comma separated list in the POST variable "queries", with the current dataset index (from 0) in the POST variable "dataset". The url can include additional variables encoded via GET.

[-tax <string>]

Path to directory containing a taxonomy database to use. [Default: '/usr/share/perl5/KronaTools/taxonomy']