Make mutation and cluster plotting single sample compatible

[graceooh]

Description

create.ccf.summary.heatmap and create.cluster.heatmap could not handle single samples. This pull request fixes this issue. It also allows create.ccf.summary.heatmap to also plot monoclonal / single sample results without erroring out.

Closes #...

Pipeline Run Results

• Case 1
  • sample:
  • input csv:
  • config:
  • output:
  • log:
• Case 2
  • sample:
  • input csv:
  • config:
  • output:
  • log:

Analysis Results

• Case 1
  • script:
  • command:
  • output:
• Case 2
  • script:
  • command:
  • output:

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]

@graceooh Can you please attach figures/file path to the single and multi sample plots generated?

[whelena]

Nice bug fix, need to trim down to avoid unnecessary hardcoded parameters.

[whelena]

For parameters added here (line 132 - 148), is everything necessary? Generally, we want to avoid hard coding project/user specific params

[whelena]

This is somewhat redundant I think, especially since users can pass through the same.as.matrix and yat arguments to BPGs create.heatmap.

[dan-knight]

If I'm understanding correctly, we can't use the result of colnames as a default argument here. This should be yaxis.lab = NULL, then set the default inside the function. Something like:

if (is.null(yaxis.lab)) {
    yaxis.lab <- colnames(x);
    }