Usage: mixcr exportPlots shmTrees [--metadata <path.(tsv|csv)>] [--node-color <meta>] [--line-color
                                  <meta>] [--node-size <meta>] [--node-label <meta>]
                                  [--alignment-nt <gene_feature>] [--alignment-aa <gene_feature>]
                                  [--alignment-no-fill] [--filter-min-nodes <n>]
                                  [--filter-min-height <n>] [--ids <id>[,<id>...]]... [--chains
                                  <chains>] [--force-overwrite] [--no-warnings] [--verbose]
                                  [--help] [[--filter-in-feature <gene_feature>]
                                  [--pattern-max-errors <n>] (--filter-aa-pattern <pattern> |
                                  --filter-nt-pattern <pattern>)] trees.shmt plots.pdf
Visualize SHM tree and save in PDF format
      trees.shmt             Input file produced by 'findShmTrees' command.
      plots.pdf              Path where to write PDF file with plots.
  -m, --metadata <path.(tsv|csv)>
                             Path to metadata file
                             Metadata should be a .tsv or .csv file with a column named 'sample'
                               with filenames of .clns files used in findShmTrees
      --node-color <meta>    Color nodes with given metadata column
      --line-color <meta>    Color lines with given metadata column
      --node-size <meta>     Size nodes with given metadata column. Predefined columns: "Abundance".
                               Default: Abundance
      --node-label <meta>    Label nodes with given metadata column. Predefined columns: "Isotype"
      --alignment-nt <gene_feature>
                             Show tree nucleotide alignments using specified gene feature
      --alignment-aa <gene_feature>
                             Show tree amino acid alignments using specified gene feature
      --alignment-no-fill    Do not highlight alignments with color
      --filter-min-nodes <n> Minimal number of nodes in tree
      --filter-min-height <n>
                             Minimal height of the tree
      --ids <id>[,<id>...]   Filter specific trees by id
      --chains <chains>      Export only trees that contains clones with specific chain (e.g. IGK,
                               IGL or IGH).
  -f, --force-overwrite      Force overwrite of output file(s).
      -nw, --no-warnings     Suppress all warning messages.
      --verbose              Verbose messages.
  -h, --help                 Show this help message and exit.
Filter by pattern
      --filter-in-feature <gene_feature>
                             Match pattern inside specified gene feature.
                               Default: CDR3
      --pattern-max-errors <n>
                             Max allowed subs & indels.
                               Default: 0
      --filter-aa-pattern <pattern>
                             Filter specific trees by aa pattern.
      --filter-nt-pattern <pattern>
                             Filter specific trees by nt pattern.
