ktImportPhymmBL - explore hierarchical metagenomic data with
zoomable pie charts
- 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.