Make mutation and cluster plotting single sample compatible #166
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graceooh
requested review from
whelena and
dan-knight
and removed request for
whelena
|
@graceooh Can you please attach figures/file path to the single and multi sample plots generated? |
whelena
reviewed
Nov 25, 2024
| @@ -118,14 +129,32 @@ create.ccf.summary.heatmap <- function( | |||
| hm.args$text.col <- ifelse(arr > contrast.thres, 'white', 'black'); | |||
| } | |||
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| if (same.as.matrix) { | |||
| hm.args$yat <- 1.5 | |||
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For parameters added here (line 132 - 148), is everything necessary? Generally, we want to avoid hard coding project/user specific params
| arr <- as.data.frame(arr) | ||
| colnames(arr) <- as.character(unique(DF$ID)) | ||
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| hm <- create.ccf.heatmap( |
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This is somewhat redundant I think, especially since users can pass through the same.as.matrix and yat arguments to BPGs create.heatmap.
whelena
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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
Analysis Results
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.
.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
mainbranch 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.mdunder the next release version or unreleased, and updated the date.Footnotes
UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records ↩
The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. ↩
Genetic information is considered PHI.
Forensic assays can identify patients with as few as 21 SNPs ↩
RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity. ↩