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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Fix text annotation #150

Closed whelena closed 1 month ago

whelena commented 1 month ago

Description

Fixing 2 main issues:

  1. Text annotations are missing from plot.
  2. Test positioning assume radial edges, need to optionally adjust for when using 'dendrogram' mode

The first problem is due to a missing segment from the old (pre-plyr) version, where line 517-546 is missing

Closes #139

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 1 month ago

Fixed issue 1 by adding a for loop.

All the force pushed is because I messed up and branched off the danknight-scalebar branch instead of main. Should be good now!

whelena commented 1 month ago

Fixed issue 2 by considering mode when adding text. The fix improves readability in dendrogram mode without affecting `radial mode

Before

Screenshot 2024-10-04 at 4 01 11 PM

After

Screenshot 2024-10-04 at 4 01 55 PM