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Add slice functions #90

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merged 9 commits into from
Aug 30, 2023
Merged

Add slice functions #90

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e6fc0ab
slice_sample()
noriakis Aug 26, 2023
6b65c0c
add slice_head()
noriakis Aug 26, 2023
92ec117
add slice_tail()
noriakis Aug 26, 2023
c2e4e42
slice_min() and slice_max()
noriakis Aug 27, 2023
6083493
update documentation
noriakis Aug 29, 2023
17eaee1
update slice_sample
noriakis Aug 30, 2023
c6d661e
Update dplyr_methods.R
noriakis Aug 30, 2023
f54c934
Update test-dplyr_methods.R
noriakis Aug 30, 2023
20fcdda
Update dplyr_methods.R
noriakis Aug 30, 2023
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4 changes: 3 additions & 1 deletion R/dplyr_methods.R
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Expand Up @@ -546,8 +546,10 @@ slice_sample.SingleCellExperiment <- function(.data, ..., n=NULL,
select(!!c_(.data)$symbol) %>%
count(!!c_(.data)$symbol)

.max_cell_count <- ifelse(nrow(count_cells)==0, 0, max(count_cells$n))

# If repeated cells due to replacement
if (count_cells$n |> max() |> gt(1)){
if (.max_cell_count |> gt(1)){
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looks good, does the warning appear in tidyseurat as well?

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Thank you for checking. Seems to be yes, although it results in an error. Should I also replace the part for tidyseurat?

> pbmc_small |> slice_sample(n=0)
Error: No cells found
In addition: Warning message:
In max(count_cells$n) : no non-missing arguments to max; returning -Inf

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@noriakis Yes, please fix the error in tidyseurat and write a unit test for it.

If this is relative to an empty object I thought you had a stop() call already.

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Thank you for your reply. The error is related to an empty object coming from stop() call in subset.Seurat() as you pointed out, so I will just fix the warnings.

message("tidySingleCellExperiment says: When sampling with replacement",
" a data frame is returned for independent data analysis.")
.data |>
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