NEWS

PCAPAM50 1.0.4 (2026-07-30)

Citation: Added package publication citation information.
Vignette title: Updated the vignette title to match the title of the associated journal publication.

the term 'misclassification' has been substituted with 'discordance' for a output diagnostic plot that highlights IHC discordance cases, with PC1-separated cases displayed along the PC1 axis.
The vignette has been updated to reflect these changes, including the revised figure.
Warning Fix: Resolved an issue where calling par(no.readonly = TRUE) in functions created an empty plot if no graphics device was active.
- Now, the functions check for an active graphics device using if (!is.null(dev.list())) before saving and restoring graphical parameters.
- on.exit(par(oldpar)) is now conditionally applied only when a device is active, ensuring unintended side effects.
- Added informative messaging (message()) when no active graphics device is detected, making the behavior transparent to users.

Renamed Parameter: Renamed inputDir to outDir for clarity and alignment with its intended purpose of storing output files.
Heatmap Enhancements: The height and width of the output heatmap are now dynamically adjusted based on the input sample size. This ensures better visualization, particularly for larger datasets.
Citation: Added citation information.