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ExportITOL

ExportITOL.Rd

Export a feature dendrogram and companion annotation files for visualisation in iTOL (Interactive Tree of Life). Produces three files:

  1. A Newick tree (<outprefix>.nwk)

  2. A colour-strip annotation coloured by NPC pathway (or any mmo$sirius_annot column) (<outprefix>_colorstrip.txt)

  3. A bar-chart annotation showing per-feature prevalence across samples (<outprefix>_barplot.txt)

Usage

ExportITOL(
  tree,
  mmo,
  outprefix = "itol_export",
  color_by = "NPC#pathway",
  palette = "Dark 3",
  na_color = "#CCCCCC"
)

Arguments

tree

Output list from FeatureDendrogram().

mmo

mmo object. Must contain mmo$sirius_annot (for colour strip) and mmo$feature_presence or mmo$feature_data (for prevalence bar chart).

outprefix

File path prefix for output files (default: "itol_export"). Directories in the path must exist.

color_by

Column name in mmo$sirius_annot used for the colour strip (default: "NPC#pathway").

palette

Qualitative palette name for colorspace::qualitative_hcl (default: "Dark 3").

na_color

Hex colour for features with no annotation (default: "#CCCCCC").

Value

Invisibly returns a named character vector of written file paths.

Details

How to load in iTOL: Upload the Newick file at https://itol.embl.de/upload.cgi, then drag and drop the two annotation files onto the displayed tree. Select "Circular" layout and enable "Display" for each dataset in the Datasets panel.

Prevalence calculation: Feature prevalence is the proportion of samples in which a feature is detected (abundance > 0). Features absent from the PA table are assigned prevalence 0. This value drives the bar-chart length in iTOL.

Colour-strip annotation: Each tip is assigned the colour of its NPC pathway (or other chosen column) from mmo$sirius_annot. Features with no annotation are coloured na_color. The legend is written into the file header so iTOL renders it automatically.

Examples

if (FALSE) {
tree <- FeatureDendrogram(mmo, distance = "dreams")
ExportITOL(tree, mmo, outprefix = "output/itol_dreams")
# Upload output/itol_dreams.nwk to iTOL, then drag and drop the two .txt files
}