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.

ktImportPhymmBL 2.8                                 June 2021                                 KTIMPORTPHYMMBL(1)