mycolorsTB
Color Palettes for Mycobacterium Tuberculosis Data Visualization
v0.1.1
·
Jul 16, 2025
·
GPL-3
Description
Colour palettes and helper functions for visualising Mycobacterium tuberculosis genomic and epidemiological data with 'ggplot2' and 'ggtree'. The package provides predefined palettes, scale functions, tree/cladogram helpers, and convenient preview tools to ensure consistent branding in pathogen-omics visualisations. The palettes were developed as part of the 'mycolorsTB' project <https://github.com/PathoGenOmics-Lab/mycolorsTB>.
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CRAN Check Status
1
ERROR
13
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| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | ERROR |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (1 non-OK)
ERROR
r-oldrel-windows-x86_64
re-building of vignette outputs
Error(s) in re-building vignettes:
--- re-building 'use-mycolors.Rmd' using rmarkdown
Quitting from use-mycolors.Rmd:77-80 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `geom_segment2()`:
! Problem while converting geom to grob.
ℹ Error occurred in the 4th layer.
Caused by error in `is.waive()`:
! could not find function "is.waive"
---
Backtrace:
▆
1. ├─base::withVisible(knit_print(x, ...))
2. ├─knitr::knit_print(x, ...)
3. └─knitr:::knit_print.default(x, ...)
4. └─knitr::normal_print(x)
5. ├─base::print(x)
6. └─ggplot2 (local) `print.ggplot2::ggplot`(x)
7. ├─ggplot2::ggplot_gtable(data)
8. └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. └─ggplot2:::by_layer(...)
10. ├─rlang::try_fetch(...)
11. │ ├─base::tryCatch(...)
12. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13.
...[truncated]...
ot2 (local) draw_geom(..., self = self)
19. └─self$geom$draw_layer(...)
20. └─ggplot2 (local) draw_layer(..., self = self)
21. └─base::lapply(...)
22. └─ggplot2 (local) FUN(X[[i]], ...)
23. ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. └─self$draw_panel(...)
25. └─ggtree (local) draw_panel(...)
26. └─ggplot2:::empty(data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'use-mycolors.Rmd' failed with diagnostics:
Problem while converting geom to grob.
ℹ Error occurred in the 4th layer.
Caused by error in `is.waive()`:
! could not find function "is.waive"
--- failed re-building 'use-mycolors.Rmd'
SUMMARY: processing the following file failed:
'use-mycolors.Rmd'
Error: Vignette re-building failed.
Execution halted
Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 10, 2026
ERROR
r-oldrel-windows-x86_64
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'use-mycolors.Rmd' using rmarkdown Quitting from use-mycolors.Rmd:77-80 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error i ...[truncated]... the 4th layer. Caused by error in `is.waive()`: ! could not find function "is.waive" --- failed re-building 'use-mycolors.Rmd' SUMMARY: processing the following file failed: 'use-mycolors.Rmd' Error: Vignette re-building failed. Execution halted
Dependency Network
Version History
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0.1.1
Mar 10, 2026