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Improved package vignette (Getting Started) for pkgdown #3

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merged 3 commits into from
Sep 19, 2023
Merged

Improved package vignette (Getting Started) for pkgdown #3

merged 3 commits into from
Sep 19, 2023

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stufield
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@stufield stufield commented Sep 18, 2023 •
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@stufield stufield requested a review from amanda-hi September 18, 2023 17:04
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This PR will run cleanly once the unit tests for plotConcord() are fixed.

amanda-hi
amanda-hi reviewed Sep 18, 2023
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vignettes/SomaPlotr.Rmd Outdated
Using `plotPDFlist()`, a PDF plot can be generated from a list of numeric
vectors, with one smoothed kernel density curve per list item:
Using `plotPDFlist()`, a PDF plot can be generated from any arbitrary _named_
list of numeric vectors, with one smoothed kernel density curve per list element:

```{r pdf-list, fig.width = 6, fig.height = 5}
list_seq <- list(seq.17138.8 = data$seq.17138.8,
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@amanda-hi amanda-hi Sep 18, 2023 •
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To avoid confusion, I'd either A) use the already log10-transformed dataset to create the list for plotPDFlist(), or B) explain that this example is starting with the "raw" RFU data, unlike the example above (for plotPDFbyGroup()) which uses the log10-transformed dataset

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@stufield stufield Sep 18, 2023 •
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Hmmm. I was trying to show the actual strength of plotPDFlist() is that it doesn't matter what kind of data you're plotting, it could be RFU, but doesn't have to be. Perhaps we should simply simulate random normals for this one?

Do you think the lapply(list_seq, log10) is unclear?

amanda-hi
amanda-hi reviewed Sep 18, 2023
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vignettes/SomaPlotr.Rmd Outdated Show resolved Hide resolved
amanda-hi
amanda-hi reviewed Sep 18, 2023
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vignettes/SomaPlotr.Rmd Outdated Show resolved Hide resolved
@stufield stufield force-pushed the improvements-pkg-vignette branch 3 times, most recently from 659cce2 to 72bed5e Compare September 19, 2023 22:50
@stufield stufield force-pushed the improvements-pkg-vignette branch from 72bed5e to 97bf8c8 Compare September 19, 2023 22:51
@stufield
Improved package vignette (Getting Started)
b4b827c 
- SomaPlotr.Rmd vignette cleanup and improvement
- word smithing and re-creating of example to better
  showcase the functionality in relation to "real" SomaScan
- setting seeds to reproduct and generate "realistic" data
- use more log10() data in examples
- fixes #2 and #6
@stufield stufield force-pushed the improvements-pkg-vignette branch from 97bf8c8 to 62ca231 Compare September 19, 2023 22:53
@stufield stufield force-pushed the improvements-pkg-vignette branch from 62ca231 to 395f5af Compare September 19, 2023 23:11
@stufield stufield merged commit 5d9f240 into main Sep 19, 2023
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@stufield stufield mentioned this pull request Sep 26, 2023
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Clean up Getting Started vignette examples
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