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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Circular angle calculations #123

Closed dan-knight closed 2 months ago

dan-knight commented 3 months ago

Description

Fixes a bug in the refactored angle calculation code to return to the original "circular" behaviour of the v1 algorithm. Before this, child angles were calculated beginning at 0 degrees, meaning that levels moved directly "downward". This creates two problems for users:

  1. Trees will naturally be more congested as nodes "bunch up" in the middle.
  2. More angles will need to be overridden by the user to address this issue.

These changes mean that the user needs to specify far fewer angles to handle crowded trees. For many use cases, the automatic angle calculation will create a well-spaced tree. Beyond this, often only one or two angles in the first level of the tree need to be overridden to create ample visual space for lower levels with many nodes.

These changes have removed the existing override.angles() function, but I haven't yet deleted the code as it be useful in the future (perhaps for handling edge cases).

Examples

radial

tree.df <- data.frame(
    parent = c(NA, 1, 2, 2, 3, 3, 3, 3, 8, 8, 8, 10, 10, 11),
    angle = NA
    );
tree.df$angle[3] <- -90;
tree.df$angle[8] <- -40;

tree <- SRCGrob(tree.df);
grid.draw(tree);
Screenshot 2024-03-28 at 1 52 15 PM

fixed

tree.df <- data.frame(
    parent = c(NA, 1, 2, 2, 3, 3, 4, 4, 6, 7, 10, 10, 7),
    angle = NA
    );
tree.df$angle[3:4] <- c(-60, 60);

tree <- SRCGrob(tree.df);
grid.draw(tree);
Screenshot 2024-03-28 at 5 04 55 PM

Closes #122

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 3 months ago

I see that there are two fucntion to calculate angles (calculate.angles.radial and calculate.angles.fixed) Althought in the exmaples you showed the two SRCGrob calls look the same. How do users choose which function to use?

dan-knight commented 3 months ago

I see that there are two fucntion to calculate angles (calculate.angles.radial and calculate.angles.fixed) Althought in the exmaples you showed the two SRCGrob calls look the same. How do users choose which function to use?

They don't! Those are all handled internally depending on the complexity of the tree. The two methods are becoming very similar anyway, so I think it would be good to combine them before releasing v3. For now, I'm just accounting for both.