When dendrogram mode is selected for trees with <6 nodes or a binary tree, calculate.clone.polygons assign angle calculation to be conducted using calculate.angle.fixed, which assumes radial mode. This PR fixes the conditions in calculate.clone.polygons so that dendrogram modes always uses calculate.angle.radial.
Closes #149
Fixed tree:
Checklist
[x] This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem[^1] - Even a small leak can be costly[^2].
[x] This PR does NOT contain germline genetic data[^3], RNA-Seq, DNA methylation, microbiome or other molecular data[^4].
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To automatically exclude such files using a .gitignore file, see here for example.
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Description
When dendrogram mode is selected for trees with <6 nodes or a binary tree,
calculate.clone.polygonsassign angle calculation to be conducted usingcalculate.angle.fixed, which assumes radial mode. This PR fixes the conditions incalculate.clone.polygonsso that dendrogram modes always usescalculate.angle.radial.Closes #149
Fixed tree:
Checklist
[x] This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
Disclosing PHI is a major problem[^1] - Even a small leak can be costly[^2].
[x] This PR does NOT contain germline genetic data[^3], RNA-Seq, DNA methylation, microbiome or other molecular data[^4].
[^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.
.png, .jpeg),.pdf,.RData,.xlsx,.doc,.ppt, or other output files.To automatically exclude such files using a .gitignore file, see here for example.
[x] I have read the code review guidelines and the code review best practice on GitHub check-list.
[x] I have set up or verified the
mainbranch protection rule following the github standards before opening this pull request.[x] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
[x] I have added the major changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.