ktImportMETAREP-EC - explore hierarchical metagenomic data with
zoomable pie charts
- Creates a Krona chart of abundances of EC (Enzyme Commission) numbers in
METAREP data folders. By default, queries with no EC number will be
ignored (see -i).
ktImportMETAREP-EC \
- [options] \ metarep_folder_1[,name_1] \ [metarep_folder_2[,name_2]] \
...
- metarep_folder
- Unpacked METAREP data folder. By default, separate datasets will be
created for each input (see [-c]).
- 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: 'metarep-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.
- [-i]
- Include a wedge for queries with no hits.
- [-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.
- [-v]
- Verbose.