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Refactor heatmaps #73

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Refactor heatmaps #73

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dan-knight
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Description

Closes #...

Checklist

  • This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
  • This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
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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:

@dan-knight dan-knight added the enhancement New feature or request label Apr 5, 2023
@dan-knight dan-knight requested a review from whelena April 5, 2023 06:29
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@whelena whelena left a comment

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I can make fixes to this PR

left.padding = 1,
right.padding = 1,
resolution = 3000,
width = 9,
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We want to make the height and width customizable since the H:W ratio depends on the number of samples and mutations


plot.cluster.hm <- function(
cluster.df,
plt.height = 6,
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We'll stick to BPG params to simplify things

legend = list(right = list(
fun = legend.ccf
)),
height = 6,
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height and width should be customizable

@dan-knight
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dan-knight commented Nov 17, 2023

EDIT: Addressed separately in #108

These functions are being picked up as S3 methods for the built-in plot function (which, of course, they aren't). This is just a naming conflict, so I can just change the names to follow BPG'screate.<plot type> standard.

…isualization into danknight-refactor-heatmaps
@dan-knight dan-knight linked an issue Nov 17, 2023 that may be closed by this pull request
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S3 plot naming conflict
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