NAME¶

ktImportEC - explore hierarchical metagenomic data with zoomable pie charts

DESCRIPTION¶

Creates a Krona chart of abundances of EC (Enzyme Commission) numbers in tab-delimited files.

ktImportEC \

[options] \ ec_numbers_1[:magnitudes_1][,name_1] \ [ec_numbers_2[:magnitudes_2][,name_2]] \ ...

ec_numbers

Tab-delimited files with EC numbers and (optionally) query IDs, magnitudes and scores. By default, query IDs, EC numbers and scores will be taken from columns 1, 2 and 3, respectively (see -q, -e, -s, and -m). 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: 'ec.krona.html']

[-n <string>]

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

[-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']

[-e <integer>]

Column of input files to use as EC number. [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.

[-i]

Include a wedge for queries with no hits.

[-d <integer>]

Maximum depth of wedges to include in the chart.

[-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.