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module data input #74

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module data input #74

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5029672
update functions for anndata input work
myushen Jul 15, 2024
3b2e1d4
update module for anndata/sce input
myushen Jul 16, 2024
6591188
merge, solve conflicts from master
myushen Jul 19, 2024
09baa87
fix
myushen Jul 19, 2024
2d78027
fix package dependency
myushen Jul 21, 2024
f2087a8
fix mt-ribsome gene identification and pipeline running
myushen Jul 23, 2024
ce36536
fix
myushen Jul 29, 2024
289a037
merge from master
myushen Jul 30, 2024
a480073
Squashed commit of the following:
myushen Aug 15, 2024
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18 changes: 17 additions & 1 deletion NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,17 @@
S3method(annotate_cell_type,HPCell)
S3method(calculate_pseudobulk,HPCell)
S3method(evaluate_hpc,HPCell)
S3method(get_single_cell,HPCell)
S3method(normalise_abundance_seurat_SCT,HPCell)
S3method(print,HPCell)
S3method(remove_dead_scuttle,HPCell)
S3method(remove_doublets_scDblFinder,HPCell)
S3method(remove_empty_DropletUtils,HPCell)
S3method(remove_empty_DropletUtils,Seurat)
S3method(remove_empty_threshold,HPCell)
S3method(remove_empty_threshold,Seurat)
S3method(score_cell_cycle_seurat,HPCell)
S3method(tranform_assay,HPCell)
export(alive_identification)
export(annotate_cell_type)
export(annotation_consensus)
Expand All @@ -18,15 +22,19 @@ export(calculate_pseudobulk)
export(cell_cycle_scoring)
export(convert_gene_names)
export(create_pseudobulk)
export(delete_lines_with_word)
export(doublet_identification)
export(empty_droplet_id)
export(empty_droplet_threshold)
export(evaluate_hpc)
export(expand_tiered_arguments)
export(factory_de_fix_effect)
export(factory_de_random_effect)
export(factory_split)
export(feature_chunks)
export(find_variable_genes)
export(get_positions)
export(get_single_cell)
export(get_unique_tissues)
export(initialise_hpc)
export(map2_test_differential_abundance_hpc)
Expand All @@ -39,20 +47,23 @@ export(map_test_differential_abundance)
export(non_batch_variation_removal)
export(normalise_abundance_seurat_SCT)
export(preprocessing_output)
export(preprocessing_output_factory)
export(pseudobulk_merge)
export(read_data_container)
export(reference_label_coarse_id)
export(reference_label_fine_id)
export(remove_dead_scuttle)
export(remove_doublets_scDblFinder)
export(remove_empty_DropletUtils)
export(remove_empty_threshold)
export(run_targets_pipeline)
export(save_experiment_data)
export(score_cell_cycle_seurat)
export(se_add_dispersion)
export(seurat_to_ligand_receptor_count)
export(split_summarized_experiment)
export(test_differential_abundance_hpc)
export(tranform_assay)
export(transform_utility)
export(vector_to_code)
exportMethods(test_differential_abundance)
import(SeuratObject)
Expand Down Expand Up @@ -119,7 +130,9 @@ importFrom(Seurat,ScaleData)
importFrom(Seurat,VariableFeatures)
importFrom(Seurat,as.Seurat)
importFrom(Seurat,as.SingleCellExperiment)
importFrom(SingleCellExperiment,"altExp<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,altExp)
importFrom(SingleR,SingleR)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"colData<-")
Expand All @@ -129,6 +142,8 @@ importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useMart)
importFrom(callr,r)
importFrom(celldex,BlueprintEncodeData)
importFrom(celldex,MonacoImmuneData)
Expand Down Expand Up @@ -224,6 +239,7 @@ importFrom(targets,tar_script)
importFrom(tibble,as_tibble)
importFrom(tibble,enframe)
importFrom(tibble,rowid_to_column)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidybulk,as_SummarizedExperiment)
importFrom(tidybulk,pivot_transcript)
Expand Down
19 changes: 18 additions & 1 deletion R/data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -27,4 +27,21 @@
#'
#' @noRd
#'
"dummy_hpc"
"dummy_hpc"


#' A data frame of Ensembl genes retrieved from biomaRt package
#'
#' This dataset contains Ensembl gene IDs, external gene names, and chromosome names
#' retrieved using the biomaRt package.
#'
#' @format A data frame map of ensembl_gene_id, external_gene_name and chromosome_name
#'
#' @usage
#' data(ensembl_genes_biomart)
#'
#' @source biomaRt::getBM()
#'
#' @keywords datasets
#' @docType data
"ensembl_genes_biomart"
26 changes: 19 additions & 7 deletions R/factories.R
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,10 @@ expand_tiered_arguments <- function(command, tiers, tiered_args) {
command_character = command |> deparse()

for(t in tiered_args){
command_character = command_character |> str_replace(t, paste0(t, "_", tiers) |> paste(collapse = ", "))
command_character = command_character |> str_replace(t, sprintf("c(%s)",
paste0(t, "_",
tiers) |>
paste(collapse = ", ")))
}

command_character |> rlang::parse_expr()
Expand All @@ -75,9 +78,10 @@ expand_tiered_arguments <- function(command, tiers, tiered_args) {


#' @importFrom stringr str_extract
#' @export
factory_split = function(
name_output, command, tiers, arguments_to_tier = c(), other_arguments_to_tier = c(),
other_arguments_to_map = c(), packages = targets::tar_option_get("packages")
other_arguments_to_map = c(), packages = targets::tar_option_get("packages") , ...
){

if(command |> deparse() |> str_detect("%>%") |> any())
Expand Down Expand Up @@ -123,7 +127,9 @@ factory_split = function(
else
resources = tar_resources(crew = tar_resources_crew(.y))


# # Process additional arguments in ...
# additional_args <- list(...)
#
tar_target_raw(
name = glue("{name_output}_{.y}") |> as.character(),
command = command |> add_tier_inputs(other_arguments_to_tier, .y),
Expand Down Expand Up @@ -204,7 +210,7 @@ factory_de_fix_effect = function(se_list_input, output_se, formula, method, tier


tar_target_raw("chunk_tbl",
pseudobulk_gran_group |>
pseudobulk_se |>
rownames() |>
feature_chunks() |>
quote()
Expand All @@ -213,7 +219,7 @@ factory_de_fix_effect = function(se_list_input, output_se, formula, method, tier

tar_target_raw(
"pseudobulk_group_list",
pseudobulk_gran_group |>
pseudobulk_se |>
group_split(!!sym(pseudobulk_group_by)) |>
quote(),
iteration = "list",
Expand Down Expand Up @@ -271,7 +277,7 @@ factory_de_random_effect = function(se_list_input, output_se, formula, tiers, fa

tar_target_raw(
"pseudobulk_group_list",
pseudobulk_gran_group |>
pseudobulk_se |>
group_split(!!sym(pseudobulk_group_by)) |>
quote(),
iteration = "list",
Expand All @@ -295,7 +301,13 @@ factory_de_random_effect = function(se_list_input, output_se, formula, tiers, fa
packages = c("tidySummarizedExperiment", "S4Vectors", "purrr", "dplyr" ,"tidybulk", "HPCell")
),

tar_target_raw("pseudobulk_table_dispersion_gene_unlist", pseudobulk_table_dispersion_gene |> unlist() |> quote(), iteration = "list"),
tar_target_raw(
"pseudobulk_table_dispersion_gene_unlist",
pseudobulk_table_dispersion_gene |> unlist() |> unlist() |> quote(),
iteration = "list"
#,
#pattern = map(pseudobulk_table_dispersion_gene) |> quote()
),

# Analyse
tar_target_raw(
Expand Down
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