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viz_targets.md

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targets

Priority level 1

  • shows clean square trees, economical with space

    • use space_test.nwk, display in < 8 vertical inches ETE: The size of every ETE graphical element can be customize (Faces). Also the margins of each face

  • capacity up to 500 easily displayed

    • use capacity_test.nwk, display and navigate in < 2 seconds ETE: it will depend on the complexity of the layout, but current tests are about 1 sec.

  • ability to display images on tips

    • use viz_sample7.nwk with thumbnails in images/ ETE: Possible using ImgFace. Can link a URL, but it will slow down the rendering. Better use local copy of the images.

  • ability to display terminal node information and link-outs

    • use viz_sample7.nwk with links in URL column of viz_sample7_data.csv ETE: Not fully implemented in the demo, but possible.

  • control tip alignment

    • use space_test.nwk, show with and without tips aligned to the right ETE: Check add_face_to_node(..., position='aligned') and TreeStyle.draw_guiding_lines

  • control line thickness and color

    • use viz_sample7.nwk with thin or thick lines ETE: Check node.img_style["hz_line_width"] and related

  • export high-resolution graphics image

    • use capacity_test.nwk, save in resolution high enough to enlarge so that names are easily readable. For successful example, see capacity_test.svg; unsuccessful example is capacity_test.jpg (resolution too low).
      ETE: PDF, SVG and PNG currently supported. Simply call tree.render("file.[png|svg|pdf]", ...)

  • supports a way to highlight clade

    • indicate "Cervidae" in viz_sample7.nwk ETE: shown in the demo. You can place random text or graphics on top of branches.
    • use vertical bar or curly brace, or enclose in colored rectangle ETE: also possible. The demo simply changes the background color of the clade

  • supports a way to distinguish multiple clades

    • indicate "Cervidae" and "Bovidae" in viz_sample7.nwk ETE: shown in the demo. You can place random text or graphics on top of branches.

  • align tips with data table

    • show viz_sample7.nwk with categorical data in trophic habit column of viz_sample7_data.csv ETE: data should be preloaded in the script, so it can accessed by the layout functions. Information can be represented as a series of aligned text faces. Check example here: http://etetoolkit.org/static/img/gallery/birds400x400.png

    • show viz_sample7.nwk with numeric data in body mass column of viz_sample7_data.csv ETE: check examples here for inspiration http://etetoolkit.org/static/img/gallery/

Priority level 2 features

  • ladderize

    • show ladder_test.nwk with and without ladderization ETE: already in the ETE API. simply call tree.ladderize()

  • ability to associate information with internal node

    • show "Cervidae" label on ancestral Cervidae node ETE: ETE reads NHX format, so any annotation can be transformed into a graphical element
    • can be static or dynamic (float-over) ETE: floating faces possible, althoug they dont always look good. Check add_face_to_node(..., position="[float|float-behind]")

  • ability to associate information with branch

    • show label "7 events" on branch leading to Cervidae
      ETE: same as before. Although ETE does not distinguish between node and branch attributes (except for node.support, which is always a branch feature.)
    • can be static or dynamic (float-over) ETE: see above

  • export vector graphics image

    • use capacity_test.nwk, see capacity_test.svg .
      ETE: tree.render("test.svg", tree_style=ts)

  • collapse clades

    • use viz_sample7.nwk, collapse Carnivora ETE: possible dynamically while rendering. Set node.img_style['draw_descendants'] = False

  • re-order clades

    • use viz_sample7.nwk, swap Cervidae and Bovidae ETE: check node.swap_children() or node.sort_descendants(), tree.sort_descendants()

Priority level 3 features

  • export annotated tree in portable tree format (e.g., NeXML, NHX, PhyloXML) ETE: NHX well supported. NexML and PhyloXML only decent support for reading.

    • (needs community standard)

  • some way to view larger trees (dynamic expansion, fish-eye, fractal, etc) ETE: not possible at the moment, but we have several experiments.

  • ability to serve as arbitrary controller

  • ability to combine phylogeny with geographic locations on a map