Hwinata add documentation

[whelena]

Description

Provide documentatio for heatmaps and clone genome distribution plot

Checklist

• 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 problem¹ - Even a small leak can be costly².

• This PR does NOT contain germline genetic data³, RNA-Seq, DNA methylation, microbiome or other molecular data⁴.

• 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.

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have set up or verified the main branch protection rule following the github standards before opening this pull request.

• 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].

• 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.

Footnotes

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. ↩

[whelena]

My R CMD check is blocked by this note:

  Skipping checking HTML validation: no command 'tidy' found

Any idea what caused this @dan-knight ?

[dan-knight]

My R CMD check is blocked by this note:

  Skipping checking HTML validation: no command 'tidy' found

This isn't actually blocking it. There are two documentation warnings caused by ...:

checking for code/documentation mismatches ... WARNING
checking Rd \usage sections ... WARNING

[whelena]

My R CMD check is blocked by this note:

  Skipping checking HTML validation: no command 'tidy' found

This isn't actually blocking it. There are two documentation warnings caused by ...:

checking for code/documentation mismatches ... WARNING
checking Rd \usage sections ... WARNING

Yes I did end up tracing it there and I have tried different ways of documenting it. I referred to BPG's documentation, which seems to pass the same tests and uses ... as well.

[dan-knight]

I referred to BPG's documentation, which seems to pass the same tests and uses ... as well.

Yeah, that's strange. I'm looking into it. We should be able to fix that and get this check to pass.

[dan-knight]

Fixed the errors. When using ..., you should:

1. Document it explicitly as a parameter
2. Include it in the usage section
3. Write usage as if you were calling the function.

Usage should be formatted as follows:

\usage{
example.function(
    arg1,
    arg2 = NULL,
    ...
    );
}

Notice that this is not written as if the function were being declared. So, don't write it as example.function <- function(arg1, arg2 = NULL);.

[whelena]

Thank you!! I don't know how I missed that but I'm glad its figured out