This function creates an HTML file containing the different figures and plots explaining the MAF dataset.
getMAFDashboard(
maf = NULL,
plotList = NULL,
outputFileName = "dashboard.html",
outputFileTitle = "MAF Dash",
outputFilePath = tempdir()
)MAF object or MAF file path information in the MAF format
A named list denoting which plots to draw. List elements can be: - boolean, if the name matches one of built-in plots: "summary_plot","burden","oncoplot","cooccurence","heatmap" - ggplot, ComplexHeatmap, or plotly object - file path to image (must be absolute path) The default value (if set to NULL) is 'list("summary_plot"=TRUE,"burden"=TRUE,"oncoplot"=TRUE,"cooccurence"=TRUE,"heatmap"=TRUE)' The order of the list determines the order of the tabs, and list names are used as tab titles.
The name of the output html dashboard file
The title of the output html dashboard
The path of the output html dashboard
No return value, the MAF dashboard html file is created in the given output folder
library(MAFDash)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
getMAFDashboard(maf = maf,outputFilePath=tempdir())
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#> processing file: MAFDash.Rmd
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#> label: setup (with options)
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#> label: read-MAF-file (with options)
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#> $ results: chr "hide"
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#> label: make-burden-plot-dot
#> Warning: `gather_()` was deprecated in tidyr 1.2.0.
#> Please use `gather()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
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#> label: make-oncoplot (with options)
#> List of 2
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#> $ fig.height: num 6
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#> All mutation types: Missense Mutation, Frame Shift Del, Nonsense
#> Mutation, Splice Site, Multi Hit, In Frame Del, Frame Shift Ins.
#> `alter_fun` is assumed vectorizable. If it does not generate correct
#> plot, please set `alter_fun_is_vectorized = FALSE` in `oncoPrint()`.
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#> label: somatic-interactions (with options)
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#> label: make-interactive-heatmap (with options)
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#> label: make-variant-table
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#> output file: /private/var/folders/jy/45byld4s14q9wc9qvbwx027m7rhngt/T/Rtmp4OcV81/file167b2c7e4961/MAFDash.knit.md
#> /usr/local/bin/pandoc +RTS -K512m -RTS /private/var/folders/jy/45byld4s14q9wc9qvbwx027m7rhngt/T/Rtmp4OcV81/file167b2c7e4961/MAFDash.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /private/var/folders/jy/45byld4s14q9wc9qvbwx027m7rhngt/T/Rtmp4OcV81/dashboard.html --lua-filter /Users/jaina13/Library/R/4.0/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Users/jaina13/Library/R/4.0/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /Users/jaina13/Library/R/4.0/library/flexdashboard/rmarkdown/templates/flex_dashboard/resources/default.html --include-in-header /var/folders/jy/45byld4s14q9wc9qvbwx027m7rhngt/T//Rtmp4OcV81/rmarkdown-str167b17039619.html --variable theme=yeti --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/jy/45byld4s14q9wc9qvbwx027m7rhngt/T//Rtmp4OcV81/rmarkdown-str167b30e58ac.html --include-in-header /var/folders/jy/45byld4s14q9wc9qvbwx027m7rhngt/T//Rtmp4OcV81/file167b22df85c5html --include-before-body /var/folders/jy/45byld4s14q9wc9qvbwx027m7rhngt/T//Rtmp4OcV81/file167b57856ef9.html --include-after-body /var/folders/jy/45byld4s14q9wc9qvbwx027m7rhngt/T//Rtmp4OcV81/file167b7938ca52.html --highlight-style pygments --include-before-body /var/folders/jy/45byld4s14q9wc9qvbwx027m7rhngt/T//Rtmp4OcV81/file167bc75a66.html --include-after-body /var/folders/jy/45byld4s14q9wc9qvbwx027m7rhngt/T//Rtmp4OcV81/file167b1fffdef0.html
#>
#> Output created: /private/var/folders/jy/45byld4s14q9wc9qvbwx027m7rhngt/T/Rtmp4OcV81/dashboard.html