ktImportTaxonomy - explore hierarchical metagenomic data with
zoomable pie charts
- 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']