NAME¶

ktImportPhymmBL - explore hierarchical metagenomic data with zoomable pie charts

DESCRIPTION¶

Creates a Krona chart of Phymm or PhymmBL results. Note: Since confidence scores are not given for species/subspecies classifications, they inheret confidence scores from genus classifications.

ktImportPhymmBL \

[options] \ phymmbl_results_1[:magnitudes_1][,name_1] \ [phymmbl_results_2[:magnitudes_2][,name_2]] \ ...

phymmbl_results

PhymmBL results files (results.03.*). Results can also be from Phymm alone (results.01.*), but [-p] must be specified. 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: 'phymm(bl).krona.html']

[-n <string>]

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

[-m <number>]

Minimum confidence. Each query sequence will only be added to taxa that were predicted with a confidence score of at least this value.

[-c]

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

[-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']

[-p]

Input is phymm only (no confidence scores).

[-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.