Figures and exports
Every plot saves as a figure that stands alone in a manuscript, and every table and result exports with a notice of where it came from and under what license, so that what leaves ClonoLoom still says how it was made.
Figures
Each plot's ⤓ button saves it as a figure:
- SVG: vector, for editing in Illustrator or Inkscape, with every color written in.
- PNG at 300 dpi, the resolution recorded in the file, so that a layout program places it at its size.
- PDF: one page of the figure's size, holding the 300-dpi image.
The figure is the plot on white whatever the window's theme, with its title and legend and a caption saying what was measured, the clonotype definition, the abundance unit, the samples, the filter, and the ClonoLoom version and day it was made. With color-vision-friendly colors on, the figure uses them too.
Exports
Export (in the Clonotypes view, the Repertoire view, or the File menu) writes a zip:
| What | File | What it holds |
|---|---|---|
| Rearrangements | rearrangements.tsv | The rows the filter keeps, as an AIRR Rearrangement TSV, each with its clonotype under the definition as clone_id |
| Clonotypes | clonotypes.csv | One row per clonotype: its chains, its total and how many samples hold it, and one column of abundance per sample |
| Diversity | diversity.csv | Every measure of every sample, with its standard error and interval |
| Rarefaction | rarefaction.csv | Every point of every curve, and the levels compared |
| Gene usage | usage.csv | Every share, by sample or condition |
| Overlap | overlap.csv, public.csv | Every pair's measures; the public clonotypes |
Each zip holds a NOTICE.txt: the files read and their SHA-256, the filter, the clonotype definition, the unit, the method, ClonoLoom's version and commit, and each public data set's license and citation. The columns of each file are in FORMATS.md.
B-cell results
Each B-cell result view has Export result. Families export complete memberships, nearest distances and exclusions; germlines export projections and reference provenance; SHM exports row/region counts and descriptive summaries; lineages export trees, nodes, sources and annotations; isotypes export usage, families, unordered pairs and observations. Each bundle contains the full result JSON, manifest, source information and notice, regardless of the displayed page or selection. Germlines and lineages include FASTA; lineages also include Newick. Blank numeric CSV fields are missing, while 0 is a measured zero. Follow the artificial immunization workflow for a complete example.
Data under terms of use
Rows of public data under a provider's terms of use (the immuneACCESS example), or under no stated license, are exported only after ClonoLoom shows those terms and you accept them, and the notice then says not to share them. Results computed from such data say to read the terms before sharing them. Your own data are yours: their notice says so.