uclahs-cds / package-CancerEvolutionVisualization

Publication Quality Phylogenetic Tree Plots
https://cran.r-project.org/web/packages/CancerEvolutionVisualization/
GNU General Public License v2.0
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Include tree and text data.frame in SRCGrob #85

Closed dan-knight closed 8 months ago

dan-knight commented 10 months ago

Description

Closes #95. Sets up export of the final tree and text data used by the plot under $input.data$tree and $input.data$text`. This differs from the input data by including any replacements to default values and data transformations as a result of the internal prep functions. Exposing this data will allow users to tweak an existing plot more easily.

At this point, there is no file export. I felt that including this functionality within the resulting plot object would allow users to use the data more flexibly. If CSV output is vital, it will be trivial to add - just another parameter and a standard write.csv() call at the end of the function.

Closes #...

Checklist

[^1]: UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records [^2]: The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. [^3]: Genetic information is considered PHI. Forensic assays can identify patients with as few as 21 SNPs [^4]: RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity.

  To automatically exclude such files using a .gitignore file, see here for example.

whelena commented 9 months ago

I approved this but don't have merge permissions, did you want to merge this to main?