Closed wvictor14 closed 1 year ago
@wvictor14 have a look at the github action; it is failing. Check maybe on your local CHECK and BiocCheck because here I have to "allow" github action each time, unfortunately. After you become a contributor, github action will be runnable by you in the future.
@wvictor14 please add your authorship details here https://docs.google.com/spreadsheets/d/19XqhN3xAMekCJ-esAolzoWT6fttruSEermjIsrOFcoo/edit?usp=sharing
@stemangiola I fixed the errors for CRAN check. There are two bioccheck errors that I am not sure best to address:
ERROR: Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags.
and
ERROR: At least 80% of man pages documenting exported objects must have runnable examples.
Also I realized that the option of inputting a tibble to order_by
argument for slice_min
and slice_max
doesn't work with the select |> slice
approach. So I added an internal function return_args
that returns the variables as symbols of such cases, that can supply the necessary columns to select
https://github.com/stemangiola/tidyseurat/pull/68/commits/7cca3f8116b4ce137c807db953d5de19f0a3d412
There are two bioccheck errors that I am not sure best to address
No problem, that could be another "challenge"
Also I realized that the option of inputting a tibble to
order_by
argument forslice_min
andslice_max
doesn't work with theselect |> slice
approach
Could you please give me minimal example ?
Also I realized that the option of inputting a tibble to
order_by
argument forslice_min
andslice_max
doesn't work with theselect |> slice
approachCould you please give me minimal example ?
This is what I mean
# in action
pbmc_small |> slice_min(tibble::tibble(nFeature_RNA, nCount_RNA), n = 2)
# return_args extracts the variables out of an expression
order_by <- expr(tibble::tibble(nFeature_RNA, nCount_RNA))
order_by_vars <- return_args(!!order_by)
# let's you input into select
pbmc_small |> select(!!!order_by_vars) |>
# and then can apply slice_min
slice_min(!!order_by, n = 6)
# A tibble: 6 × 2
nFeature_RNA nCount_RNA
<int> <dbl>
1 26 51
2 29 157
3 29 172
4 30 150
5 30 202
6 31 62
Not sure if there is a more straightforward way, or how to make it more robust. What do you think?
Also I realized that the option of inputting a tibble to
order_by
argument forslice_min
andslice_max
doesn't work with theselect |> slice
approachCould you please give me minimal example ?
This is what I mean
# in action pbmc_small |> slice_min(tibble::tibble(nFeature_RNA, nCount_RNA), n = 2) # return_args extracts the variables out of an expression order_by <- expr(tibble::tibble(nFeature_RNA, nCount_RNA)) order_by_vars <- return_args(!!order_by) # let's you input into select pbmc_small |> select(!!!order_by_vars) |> # and then can apply slice_min slice_min(!!order_by, n = 6) # A tibble: 6 × 2 nFeature_RNA nCount_RNA <int> <dbl> 1 26 51 2 29 157 3 29 172 4 30 150 5 30 202 6 31 62
Not sure if there is a more straightforward way, or how to make it more robust. What do you think?
Great! I left a last comment to address (Above) and then this PR is on its way!
A detail. In the tidy transcriptomics framework, we adopt the standard of, no abbreviations and no acronyms.
Would you mind changing return_args into a self-explanatory function name, e.g. return_argumentsof... or anything else that would make sense.
This also applies to any variable, e.g. args_expr, args_vars, ...
I think I got them all!
Thanks a lot @wvictor14 for your PR! Well done.
Now that you are an expert, if you want to translate your PR to the other tidy adapters tidySingleCellExperiment
and/or tidySummarizedExperiment
feel free, that would be welcome!
No expectations of course.
Hi I found this issue on tidyomics and thought it would be good experience to try
Let me know how it looks and if there's any changes needed
This adds the slice_ family: