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fixes #250

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merged 1 commit into from
Jul 23, 2022
Merged

fixes #250

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1 change: 1 addition & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,7 @@ importFrom(purrr,as_mapper)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map2_dfr)
importFrom(purrr,map_chr)
importFrom(purrr,map_dfr)
importFrom(purrr,map_lgl)
importFrom(purrr,reduce)
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30 changes: 19 additions & 11 deletions R/methods_SE.R
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Expand Up @@ -926,7 +926,7 @@ setMethod("aggregate_duplicates",



#' @importFrom rlang quo_is_symbol
#' @importFrom rlang quo_is_symbolic
.deconvolve_cellularity_se = function(.data,
reference = X_cibersort,
method = "cibersort",
Expand All @@ -944,7 +944,7 @@ setMethod("aggregate_duplicates",
.[[get_assay_scaled_if_exists_SE(.data)]] %>%

# Change row names
when(quo_is_symbol(.transcript) ~ {
when(quo_is_symbolic(.transcript) ~ {
.x = (.)
rownames(.x) = .data %>% pivot_transcript() %>% pull(!!.transcript)
.x
Expand Down Expand Up @@ -1294,6 +1294,8 @@ setMethod("keep_variable",
#' keep_variable
#' @inheritParams keep_variable
#'
#' @importFrom purrr map_chr
#'
#' @docType methods
#' @rdname keep_variable-methods
#'
Expand All @@ -1319,10 +1321,10 @@ setMethod("keep_variable",
# Check factor_of_interest
if(
!is.null(factor_of_interest) &&
quo_is_symbol(factor_of_interest) &&
(quo_name(factor_of_interest) %in% colnames(colData(.data)) %>% not())
quo_is_symbolic(factor_of_interest) &&
(quo_names(factor_of_interest) %in% colnames(colData(.data)) |> all() %>% not())
)
stop(sprintf("tidybulk says: the column %s is not present in colData", quo_name(factor_of_interest)))
stop(sprintf("tidybulk says: the column %s is not present in colData", quo_names(factor_of_interest)))

if (minimum_counts < 0)
stop("The parameter minimum_counts must be > 0")
Expand All @@ -1343,16 +1345,22 @@ setMethod("keep_variable",

factor_of_interest %>%
when(
quo_is_symbol(factor_of_interest) &&
quo_is_symbolic(factor_of_interest) &&
(
colData(.data)[, quo_name(factor_of_interest)] %>%
class %in% c("numeric", "integer", "double")) ~
colData(.data)[, quo_names(factor_of_interest), drop=FALSE] |>
as_tibble() |>
map_chr(~class(.x)) %in% c("numeric", "integer", "double") |>
any()
) ~
{
message("tidybulk says: The factor of interest is continuous (e.g., integer,numeric, double). The data will be filtered without grouping.")
message("tidybulk says: The factor(s) of interest include continuous variable (e.g., integer,numeric, double). The data will be filtered without grouping.")
NULL
},
quo_is_symbol(factor_of_interest) ~
colData(.data)[, quo_name(factor_of_interest)],
quo_is_symbolic(factor_of_interest) ~
colData(.data)[, quo_names(factor_of_interest), drop=FALSE] |>
as_tibble() |>
unite("factor_of_interest") |>
pull(factor_of_interest),
~ NULL
)

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1 change: 0 additions & 1 deletion tests/testthat/test-bulk_methods_SummarizedExperiment.R
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Expand Up @@ -4,7 +4,6 @@ data("se_mini")
data("breast_tcga_mini_SE")

input_df = setNames(se_mini %>% tidybulk() %>% as_tibble(), c( "b","a", "c", "Cell type", "time" , "condition", "days", "dead", "entrez"))

input_df_breast = setNames( breast_tcga_mini_SE %>% tidybulk() %>% as_tibble(), c( "b", "a","c", "c norm", "call" ))

test_that("tidybulk SummarizedExperiment conversion",{
Expand Down