KTIMPORTMGRAST

NAME

ktImportMGRAST - explore hierarchical metagenomic data with zoomable pie charts

DESCRIPTION

Creates a Krona chart from MG-RAST organism or functional analyses.

ktImportMGRAST \

[options] \ mgrast_table_1[,name_1] \ [mgrast_table_2[,name_2]] \ ...

mgrast_table

A table exported from MG-RAST. It can be from organism or functional analysis, but all tables being imported should be consistent. 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: ’mg-rast.krona.html’]

[-n <string>]

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

[-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]

Use percent identity for average scores instead of log[10] e-value.

[-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.