Polish the get-started guide #97
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| This vignettes provides a quick introduction to the **{laminr}** workflow. | ||
| For more details about how **{laminr}** works see `vignette("concepts_features", package = "laminr")`. |
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This sentence now comes at the very end of the tutorial so that users don't lose time reading boilerplate.
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| Some functionality requires additional packages. |
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I think it's super critical that connecting on the command line to configure the default instance comes now.
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| See the "Initial setup" section of `vignette("concepts_features", package = "laminr")` for more details. | ||
| This instance acts as the default instance for everything that follows. |
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I hope this is clear enough. If another sentence is needed please add.
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| # Track data provenance | ||
| # Track data lineage |
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People should get used to calling track() first thing.
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| # Start an R session | ||
| # Connect to the default instance |
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I find it problematic to say "connect to the default instance" in this heading, @lazappi, because that just happened 3 lines above on the command line. Don't you agree?
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This is how it reads now:
I felt that if one calls it "Start an R session" and then people see that they create an instance object by calling connect() in R one avoids calling two different things (CLI connect vs R connect()) with the same name "connect to the default instance".
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| # Set cell identities to the provided cell type annotation | ||
| SeuratObject::Idents(seurat) <- "cell_type" | ||
| # Normalise the data | ||
| seurat <- Seurat::NormalizeData(seurat) |
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I thought that this let's peoples memory and storage explode; that's why I removed it. It'd be a bad experience if upload or compute etc. took long -- so keeping data small would be good.
If it's not actually an issue anymore, it's all good!
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Also, I'm seeing an inconsistent level, will fix this: 
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I will also style the UID here with backticks: 
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Why is the default instance here 
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The most important change here is establishing a clearer and simpler order within the setup section.
I'd almost be tempted to install laminr after doing the python stuff, but I left it like it was for now.