This repo provides a function for creating Krona charts in R.
- The interactive charts can be explored directly within R-Markdown documents in RStudio and will be embedded into documents rendered to HTML webpages.
- For document formats like PDF, DOCX, ODT, etc., snapshot images will be inserted.
- Support for phyloseq objects.
- Flexible grouping into multiple datasets explored within the same chart
- Custom coloring schemes
The following snapshot image of a Krona chart gives an overview of the taxa in the GlobalPatterns dataset from phyloseq package. It was generated in the example analysis.
A small tutorial is provided in the example R-Markdown document. Two rendered versions can be downloaded:
- A HTML webpage with embedded interactive charts
- A PDF document
For a documentation of all possible options for plot_krona see the R
script.
Whether interactive charts or static snapshots are embedded depends on
whether the plot_krona function is executed from within R-Markdown
chunks, in the R console or rendered to different document
formats. Snapshots can be
enforced with snapshot=TRUE.
| interactive chart | snapshot image* | remarks | |
|---|---|---|---|
| Inline view below R-Markdown chunks (Rstudio) | yes | yes (png) | (1) interactive chart size can be changed with iframe_width / iframe_height, but this just adds scrollbars, the viewport does not change. (2) Snapshots (with snapshot=TRUE) can appear too large since expanded to 100% width. (3) out.width / out.height chunk options have no effect |
| R console | yes (in browser) | yes (image viewer) | set display=FALSE for simple conversion without viewing |
| HTML (html_document) | yes | yes (png, pdf) | (1) interactive chart: iframe_height modifies the height (e.g. 600px); (2) if snapshots appear too small, either increase snapshot_dim or set out.width (e.g. to 90%) to zoom in. |
| PDF (pdf_document) | - | yes (png, pdf) | control size with snapshot_dim |
| DOCX (word_document) | - | yes (png, pdf) | Figures always have the same (incorrect) size |
| OpenDocument Text (odt_document) | - | yes (png, pdf) | Set out.width to same value as width in snapshot_dim (e.g.: out.width='6in'). Otherwise, the figure will be huge. |
| RTF text (rtf_document) | - | yes (png) | see ODT |
| Github Markdown (github_document) | (yes) | yes | See HTML; interactive charts not displayed on Github (use snapshots) |
* snapshot_format values can be png, pdf or jpeg, however jpeg
rarely works, produces a black background with many formats