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Tweak print method to show altExpNames #85

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Tweak print method to show altExpNames #85

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5ac207e
test change print_method.R
Biomiha Aug 23, 2023
c1db700
Update print_method.R
Biomiha Aug 23, 2023
5a5b71b
Update print_method.R
Biomiha Aug 23, 2023
67a48f0
Update print_method.R
Biomiha Aug 23, 2023
56da331
Merge branch 'master' into new-altExpNames
Biomiha Aug 23, 2023
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89 changes: 42 additions & 47 deletions R/print_method.R
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
# This file is a replacement of the unexported functions in the tibble package, in order to specify "tibble abstraction in the header"
# This file is a replacement of the unexported functions in the tibble
# package, in order to specify "tibble abstraction in the header"

#' @name tbl_format_header
#' @rdname tbl_format_header
Expand All @@ -13,62 +14,56 @@
#' @importFrom pillar style_subtle
#' @importFrom pillar tbl_format_header
#' @export
tbl_format_header.tidySingleCellExperiment <- function(x, setup, ...){

number_of_features = x |> attr("number_of_features")
assay_names = x |> attr("assay_names")

named_header <- setup$tbl_sum

# Change name
names(named_header) = "A SingleCellExperiment-tibble abstraction"

if (all(names2(named_header) == "")) {
header <- named_header
}
else {
header <-
paste0(
align(paste0(names2(named_header), ":"), space = NBSP),
" ",
named_header
) %>%

# Add further info single-cell
append(sprintf(
"\033[90m Features=%s | Cells=%s | Assays=%s\033[39m",
number_of_features,
nrow(x),
assay_names %>% paste(collapse=", ")
), after = 1)
}

style_subtle(pillar___format_comment(header, width = setup$width))

tbl_format_header.tidySingleCellExperiment <- function(x, setup, ...) {

number_of_features <- x |> attr("number_of_features")
assay_names <- x |> attr("assay_names")
altExpNames <- x |> attr("altExpNames")

# Change name
named_header <- setup$tbl_sum
names(named_header) <- "A SingleCellExperiment-tibble abstraction"

if (all(names2(named_header) == "")) {
header <- named_header
} else {
header <- paste0(
align(paste0(names2(named_header), ":"), space=NBSP),
" ", named_header) %>%
# Add further info single-cell
append(sprintf(
"\033[90m Features=%s | Cells=%s | Assays=%s | altExpNames=%s\033[39m",
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Thanks.

I bit more elegant would be

  • Replace altExpNames with Assays_alternative
  • Conditionally add "| altExpNames=%s" if alternative experiment exists

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Fair point. I had considered adding the information on a conditional basis but personally I prefer to know even if it's empty. The standard SCE print method outputs altExpNames(0): when empty and altExpNames(1): Antibody Capture when it is populated (Antibody Capture being the name of the alternative experiment and can be any string). If you feel you would rather keep it only when it is non-NULL I can do that quite easily.
In relation to the naming, it actually refers to the name of the experiment rather than the names of the assays, i.e. if it exists you will still have counts and normcounts or other as the assay names within the altExp slot. How about saying Other_experiments=?
I will also add the unit tests and other missing bits whilst I am at it.

Thanks.

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@stemangiola stemangiola Aug 24, 2023 •
edited
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I see.

let's try to generalise the concept of experiment and assay, still hinting at the non-modular nature of singlecellexperiment.

So I am in favour of printing the experiments within the object, if they are 1,2,3, independently whether they are base or alternative.

having said that, there are a lot of ways to go about that. One possibility is to do

Assays= base:counts,logcounts; Antibody capture:counts,logcounts; ADT:counts

Other ideas are welcome!

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@stemangiola stemangiola Aug 25, 2023 •
edited
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@Biomiha, I realised that the sentence "OK, the goal here is to provide an interface that promotes modularity. " sounded very bad in writing; the tone I was thinking was completely different from how you would read it!

I used a poor form to give the broad indication that "the tidy transcriptomics thrives to giving modularity (which sometimes diverges from the Bioc framework)."

I hope you did not take it personally!

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No dude, absolutely not. I work in biotech 😄 .
I agree with what you've said. Am working on implementation, just been very busy lately.

number_of_features, nrow(x),
paste(assay_names, collapse=", "),
if(length(nchar(altExpNames)) > 0) paste(altExpNames, collapse=", ") else {"NULL"}
), after=1)
}
style_subtle(pillar___format_comment(header, width=setup$width))
}

#' @name formatting
#' @rdname formatting
#' @aliases print
#' @inherit tibble::formatting
#' @return Prints a message to the console describing
#' the contents of the `tidySingleCellExperiment`.
#'
#' @examples
#' data(pbmc_small)
#' print(pbmc_small)
#'
#' @importFrom vctrs new_data_frame
#' @importFrom SummarizedExperiment assayNames
#' @importFrom SingleCellExperiment altExpNames
#' @export
print.SingleCellExperiment <- function(x, ..., n = NULL, width = NULL) {#, n_extra = NULL) {
# TODO: argument 'n_extra' seems to not
# exist anymore; see ?tibble::print.tbl

x |>
as_tibble(n_dimensions_to_return = 5 ) |>

new_data_frame(class = c("tidySingleCellExperiment", "tbl")) %>%
add_attr( nrow(x), "number_of_features") %>%
add_attr( assays(x) %>% names , "assay_names") %>%

print()

invisible(x)
print.SingleCellExperiment <- function(x, ..., n=NULL, width=NULL) {
x |>
as_tibble(n_dimensions_to_return=5) |>
new_data_frame(class=c("tidySingleCellExperiment", "tbl")) %>%
add_attr(nrow(x), "number_of_features") %>%
add_attr(assayNames(x), "assay_names") %>%
add_attr(altExpNames(x), "altExpNames") %>%
print()

invisible(x)
}