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Update confounders and filtering #318

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merged 2 commits into from
Dec 13, 2024
Merged

Update confounders and filtering #318

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c7b4eae
use a function to drop env
stemangiola Dec 13, 2024
b04680a
add design to filtering
stemangiola Dec 13, 2024
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2 changes: 2 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -155,13 +155,15 @@ importFrom(rlang,enquo)
importFrom(rlang,enquos)
importFrom(rlang,flatten_if)
importFrom(rlang,inform)
importFrom(rlang,is_quosure)
importFrom(rlang,is_spliced)
importFrom(rlang,quo)
importFrom(rlang,quo_is_missing)
importFrom(rlang,quo_is_null)
importFrom(rlang,quo_is_symbol)
importFrom(rlang,quo_is_symbolic)
importFrom(rlang,quo_name)
importFrom(rlang,quo_set_env)
importFrom(rlang,quo_squash)
importFrom(rlang,set_names)
importFrom(scales,extended_breaks)
Expand Down
22 changes: 14 additions & 8 deletions R/methods.R
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Expand Up @@ -477,10 +477,10 @@ setGeneric("scale_abundance", function(.data,

# Attach column internals
add_tt_columns(
!!.sample,
!!.transcript,
!!.abundance,
!!(function(x, v) enquo(v))(x,!!value_scaled)
!!(.sample |> drop_enquo_env()),
!!(.transcript |> drop_enquo_env()),
!!(.abundance |> drop_enquo_env()),
!!(((function(x, v) enquo(v))(x,!!value_scaled)) |> drop_enquo_env())
)


Expand Down Expand Up @@ -698,10 +698,10 @@ setGeneric("quantile_normalise_abundance", function(.data,

# Attach column internals
add_tt_columns(
!!.sample,
!!.transcript,
!!.abundance,
!!(function(x, v) enquo(v))(x,!!value_scaled)
!!(.sample |> drop_enquo_env()),
!!(.transcript |> drop_enquo_env()),
!!(.abundance |> drop_enquo_env()),
!!(((function(x, v) enquo(v))(x,!!value_scaled)) |> drop_enquo_env())
)


Expand Down Expand Up @@ -3132,6 +3132,7 @@ setGeneric("identify_abundant", function(.data,
.transcript = NULL,
.abundance = NULL,
factor_of_interest = NULL,
design = NULL,
minimum_counts = 10,
minimum_proportion = 0.7)
standardGeneric("identify_abundant"))
Expand All @@ -3142,6 +3143,7 @@ setGeneric("identify_abundant", function(.data,
.transcript = NULL,
.abundance = NULL,
factor_of_interest = NULL,
design = NULL,
minimum_counts = 10,
minimum_proportion = 0.7)
{
Expand Down Expand Up @@ -3250,6 +3252,7 @@ setGeneric("identify_abundant", function(.data,
edgeR::filterByExpr(
min.count = minimum_counts,
group = string_factor_of_interest,
design = design,
min.prop = minimum_proportion
) %>%
not() |>
Expand Down Expand Up @@ -3345,6 +3348,7 @@ setGeneric("keep_abundant", function(.data,
.transcript = NULL,
.abundance = NULL,
factor_of_interest = NULL,
design = NULL,
minimum_counts = 10,
minimum_proportion = 0.7)
standardGeneric("keep_abundant"))
Expand All @@ -3355,6 +3359,7 @@ setGeneric("keep_abundant", function(.data,
.transcript = NULL,
.abundance = NULL,
factor_of_interest = NULL,
design = NULL,
minimum_counts = 10,
minimum_proportion = 0.7)
{
Expand Down Expand Up @@ -3387,6 +3392,7 @@ setGeneric("keep_abundant", function(.data,
.transcript = !!.transcript,
.abundance = !!.abundance,
factor_of_interest = !!factor_of_interest,
design = design,
minimum_counts = minimum_counts,
minimum_proportion = minimum_proportion
) |>
Expand Down
25 changes: 14 additions & 11 deletions R/methods_SE.R
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Expand Up @@ -196,7 +196,7 @@ setMethod("tidybulk", "RangedSummarizedExperiment", .tidybulk_se)
memorise_methods_used(c("edger", "tmm")) %>%

# Attach column internals
add_tt_columns(.abundance_scaled = !!(function(x, v) enquo(v))(x,!!as.symbol(value_scaled)))
add_tt_columns(.abundance_scaled = !!(((function(x, v) enquo(v))(x,!!as.symbol(value_scaled))) |> drop_enquo_env()) )

}

Expand Down Expand Up @@ -321,7 +321,7 @@ setMethod("scale_abundance",
memorise_methods_used(c("quantile")) %>%

# Attach column internals
add_tt_columns(.abundance_scaled = !!(function(x, v) enquo(v))(x,!!as.symbol(value_scaled)))
add_tt_columns(.abundance_scaled = !!(((function(x, v) enquo(v))(x,!!as.symbol(value_scaled))) |> drop_enquo_env()) )

}

Expand Down Expand Up @@ -953,8 +953,7 @@ setMethod("remove_redundancy",
memorise_methods_used("sva") %>%

# Attach column internals
add_tt_columns(.abundance_adjusted = !!(function(x, v)
enquo(v))(x, !!as.symbol(value_adjusted)))
add_tt_columns(.abundance_adjusted = !!(((function(x, v) enquo(v))(x,!!as.symbol(value_adjusted))) |> drop_enquo_env()) )

}

Expand Down Expand Up @@ -1573,6 +1572,7 @@ setMethod("keep_variable",
.transcript = NULL,
.abundance = NULL,
factor_of_interest = NULL,
design = NULL,
minimum_counts = 10,
minimum_proportion = 0.7)
{
Expand Down Expand Up @@ -1680,6 +1680,7 @@ setMethod("keep_variable",
edgeR::filterByExpr(
min.count = minimum_counts,
group = string_factor_of_interest,
design = design,
min.prop = minimum_proportion,
lib.size = Matrix::colSums(., na.rm=TRUE)
) %>%
Expand Down Expand Up @@ -1727,6 +1728,7 @@ setMethod("identify_abundant",
.transcript = NULL,
.abundance = NULL,
factor_of_interest = NULL,
design = NULL,
minimum_counts = 10,
minimum_proportion = 0.7)
{
Expand All @@ -1746,7 +1748,8 @@ setMethod("identify_abundant",
factor_of_interest = !!factor_of_interest,
minimum_counts = minimum_counts,
minimum_proportion = minimum_proportion,
.abundance = !!.abundance
.abundance = !!.abundance,
design = design
)

.data[rowData(.data)$.abundant,]
Expand Down Expand Up @@ -2819,14 +2822,14 @@ setMethod("describe_transcript", "RangedSummarizedExperiment", .describe_transcr
#' @importFrom SummarizedExperiment as.data.frame
.resolve_complete_confounders_of_non_interest <- function(se, ...){

colData(se) =
colData(se) |>
as.data.frame() |>
.resolve_complete_confounders_of_non_interest_df(...) |>
colData(se) =
colData(se) |>
as.data.frame() |>
.resolve_complete_confounders_of_non_interest_df(...) |>
DataFrame()

se

}

#' resolve_complete_confounders_of_non_interest
Expand Down
28 changes: 28 additions & 0 deletions R/utilities.R
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Expand Up @@ -1514,3 +1514,31 @@ check_and_install_packages <- function(packages) {
)
}
}

#' Drop Environment from a Quosure
#'
#' Takes a quosure and resets its environment to `emptyenv()` without altering
#' its expression.
#'
#' @param q A quosure object to have its environment stripped.
#' @return A quosure with the same expression but environment set to `emptyenv()`.
#'
#' @importFrom rlang is_quosure
#' @importFrom rlang quo_set_env
#'
#' @examples
#' library(rlang)
#'
#' q <- quo(x + y)
#' environment(q)
#'
#' q_stripped <- drop_enquo_env(q)
#' identical(quo_get_env(q_stripped), emptyenv()) # TRUE
#'
#' @noRd
drop_enquo_env <- function(q) {
if (!rlang::is_quosure(q)) {
stop("`q` must be a quosure.")
}
rlang::quo_set_env(q, emptyenv())
}
6 changes: 6 additions & 0 deletions man/identify_abundant-methods.Rd
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6 changes: 6 additions & 0 deletions man/keep_abundant-methods.Rd
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14 changes: 7 additions & 7 deletions man/resolve_complete_confounders_of_non_interest.Rd
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