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
[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].
[x] This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g..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 set up or verified the main branch 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.md under the next release version or unreleased, and updated the date.
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
[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
main
branch 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.md
under the next release version or unreleased, and updated the date.