Assess sequencing results

Usage

assess_run(
  metadata = NULL,
  asvtable = NULL,
  wells = "Well",
  plate = NULL,
  category = NULL,
  minReadCount = 0,
  pcoa = FALSE,
  corrplot = FALSE,
  ...
)

Arguments

metadata: metadata object
asvtable: asvtable object
wells: wells for each sample. Expecting A01, A02, etc.
plate: plate samples were on. Can be left as NULL if there's only one plate.
category: Varible to label wells by. Makes the most sense if positive and negative controls are labeled.
minReadCount: Minimum number of total reads for sample to be kept. Recommend to keep it at 0, but can change that if you want.
pcoa: Include PCoA data (can significantly increase run time, so set to FALSE by default)
corrplot: Generate correlation plots. Set to FALSE by default as for now not sure how helpful it actually is
...: Allows passing of arguments to nested functions. not being used at the moment.

Value

figures visualizing results

Examples

out <- micro4R::assess_example
met <- out$metadata
asv <- out$asvtable
assess_run(metadata = met, asvtable = asv, wells = "well", plate = "Plate", category = "SampleType")
#> 
#> 
#> processing file: test.Rmd
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#> 2/4 [setup]  
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#> 4/4 [example]



#> output file: test.knit.md
#> /opt/hostedtoolcache/pandoc/3.1.11/x64/pandoc +RTS -K512m -RTS test.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output test.html --lua-filter /home/runner/work/_temp/Library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/runner/work/_temp/Library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/runner/work/_temp/Library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpCCzUxF/rmarkdown-str1e747e06de52.html 
#> 
#> Output created: test.html