ktImportFCP - explore hierarchical metagenomic data with zoomable
pie charts
Creates a Krona chart based on the results of FCP (Fragment
Classification Package).
ktImportFCP \
- [options] \ fcp_output_1[:magnitudes_1][,name_1] \
[fcp_output_2[:magnitudes_2][,name_2]] \ ...
- fcp_output
- Results of running any FCP classification tool (except BLASTN.py, which
only outputs raw BLAST results). 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: 'fcp.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.
- [-d <integer>]
- Maximum depth of wedges to include in the chart.
- [-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.