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refactor setupMapMyCells
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@UCDNJJ
UCDNJJ committed Nov 18, 2024
1 parent 2aac488 commit 06b97dd
Showing 1 changed file with 34 additions and 36 deletions.
70 changes: 34 additions & 36 deletions R/setupMapMyCells.R
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Original file line number Diff line number Diff line change
Expand Up @@ -30,42 +30,40 @@ addMapMyCells = function(AIT_anndata,

tryCatch(
{
# move to zzz try catch
## move to zzz try catch
cell_type_mapper <- import("cell_type_mapper")
temp_folder = tmp_dir
mode = AIT_anndata$uns$mode

if ((length(AIT_anndata$uns$hierarchical[[mode]]) > 0) && force==FALSE) {
stop(paste0(paste0("ERROR: mode provided '", mode),
if ((length(AIT_anndata$uns$hierarchical[[AIT_anndata$uns$mode]]) > 0) && force==FALSE) {
stop(paste0(paste0("ERROR: mode provided '", AIT_anndata$uns$mode),
"' already exists, choose a new mode name or use force=TRUE to overwrite."))
}

if((length(hierarchy)==0)|(sum(class(hierarchy)=="list")<1)){
stop("hierarchy must be a list of term_set_labels in the reference taxonomy ordered from most gross to most fine included in AIT_anndata or provided separately.")
}

if (is.null(temp_folder) || temp_folder == "") {
temp_folder <- paste0("temp_folder_", format(Sys.time(), "%Y%m%d-%H%M%S"))
temp_folder <- file.path(getwd(), temp_folder)
dir.create(temp_folder)
if (is.null(tmp_dir) || tmp_dir == "") {
tmp_dir <- paste0("tmp_dir_", format(Sys.time(), "%Y%m%d-%H%M%S"))
tmp_dir <- file.path(getwd(), tmp_dir)
dir.create(tmp_dir)
}

# get an ordered list of taxonomy's hierarchy levels.
taxonomy_hierarchy = get_hierarchy(AIT_anndata, hierarchy)

# get file path to the AIT taxonomy (h5ad)
taxonomy_anndata_path = file.path(AIT_anndata$uns$taxonomyDir, paste0(AIT_anndata$uns$title, ".h5ad"))
anndata_path = get_anndata_path(taxonomy_anndata_path, temp_folder)
anndata_path = get_anndata_path(taxonomy_anndata_path, tmp_dir)

# (NEW!) write a subsetted h5ad file to the temp_folder. This will allow proper subsetting of the compute stats and speed it up.
if(sum(AIT.anndata$uns$filter[[mode]])==0){
# (NEW!) write a subsetted h5ad file to the tmp_dir. This will allow proper subsetting of the compute stats and speed it up.
if(sum(AIT.anndata$uns$filter[[AIT_anndata$uns$mode]])==0){
anndata_calc_path = anndata_path
AIT_anndata_calc = AIT_anndata
} else {
mode_dir <- file.path(AIT_anndata$uns$taxonomyDir, "temp")
anndata_calc_path <- file.path(mode_dir, paste0(AIT_anndata$uns$title, ".h5ad"))
dir.create(mode_dir)
keep <- !(AIT_anndata$uns$filter[[mode]])
keep <- !(AIT_anndata$uns$filter[[AIT_anndata$uns$mode]])
AIT_anndata_calc <- AIT_anndata[keep,]
AIT_anndata_calc$uns$taxonomyDir <- mode_dir
AIT_anndata_calc$write_h5ad(anndata_calc_path)
Expand All @@ -78,23 +76,23 @@ addMapMyCells = function(AIT_anndata,
# compute stats and save them to anndata.
precomp_stats_output_path = user_precomp_stats_path
if(is.null(precomp_stats_output_path)) {
precomp_stats_output_path = run_precomp_stats(taxonomy_anndata_path, n_processors, normalization, temp_folder, taxonomy_hierarchy)
precomp_stats_output_path = run_precomp_stats(taxonomy_anndata_path, n_processors, normalization, tmp_dir, taxonomy_hierarchy)
}
AIT_anndata = save_precomp_stats_to_uns(taxonomy_anndata_path, precomp_stats_output_path, AIT_anndata$uns$mode)

# compute query markers and save them to anndata
query_markers_output_path = user_query_markers_path
if(is.null(query_markers_output_path)) {
print("run_reference_markers")
ref_markers_file_path = run_reference_markers(precomp_stats_output_path, n_processors, temp_folder)
ref_markers_file_path = run_reference_markers(precomp_stats_output_path, n_processors, tmp_dir)
print("run_query_markers")
query_markers_output_path = run_query_markers(anndata_calc_path, ref_markers_file_path, n_processors, temp_folder)
query_markers_output_path = run_query_markers(anndata_calc_path, ref_markers_file_path, n_processors, tmp_dir)
}
AIT_anndata_calc = save_query_markers_to_uns(AIT_anndata_calc, query_markers_output_path) # Move back to original file

# (NEW!) Move stats from calculation anndata to actual anndata
AIT_anndata$uns$hierarchical[[mode]][["precomp_stats"]] <- AIT_anndata_calc$uns$hierarchical[[mode]][["precomp_stats"]]
AIT_anndata$uns$hierarchical[[mode]][["query_markers"]] <- AIT_anndata_calc$uns$hierarchical[[mode]][["query_markers"]]
AIT_anndata$uns$hierarchical[[AIT_anndata$uns$mode]][["precomp_stats"]] <- AIT_anndata_calc$uns$hierarchical[[AIT_anndata$uns$mode]][["precomp_stats"]]
AIT_anndata$uns$hierarchical[[AIT_anndata$uns$mode]][["query_markers"]] <- AIT_anndata_calc$uns$hierarchical[[AIT_anndata$uns$mode]][["query_markers"]]

# Overwrite correct anndata with added query markers
AIT_anndata$write_h5ad(anndata_path)
Expand All @@ -106,8 +104,8 @@ addMapMyCells = function(AIT_anndata,
finally = {
# remove the temp folder is it was code generated
if (is.null(tmp_dir) || tmp_dir == "") {
print(paste("Deleting temp folder", temp_folder))
unlink(temp_folder, recursive = TRUE)
print(paste("Deleting temp folder", tmp_dir))
unlink(tmp_dir, recursive = TRUE)
}
else {
# remove the files is they were code generated
Expand Down Expand Up @@ -139,24 +137,24 @@ addMapMyCells = function(AIT_anndata,
#' @param anndata_path Local file path of the AIT reference taxonomy (h5ad file).
#' @param n_processors Number of independent worker processes to spin up.
#' @param normalization Normalization of the h5ad files; must be either 'raw' or 'log2CPM'.
#' @param temp_folder Temporary directory for writing out the hierarchical files (the code will clean these up after itself).
#' @param tmp_dir Temporary directory for writing out the hierarchical files (the code will clean these up after itself).
#' @param hierarchy List of term_set_labels in the reference taxonomy ordered from most gross to most fine.
#'
#' @return File path to the precompute stats file.
#'
#' @keywords internal
run_precomp_stats = function(anndata_path, n_processors, normalization, temp_folder, hierarchy) {
run_precomp_stats = function(anndata_path, n_processors, normalization, tmp_dir, hierarchy) {

##
temp_precomp_stats_name = paste0("precomp_stats_", format(Sys.time(), "%Y%m%d-%H%M%S"))
precomp_stats_filename <- paste0(temp_precomp_stats_name, ".h5")
precomp_stats_output_path <- file.path(temp_folder, precomp_stats_filename)
precomp_stats_output_path <- file.path(tmp_dir, precomp_stats_filename)

precomp_stats_config <- list(
'h5ad_path' = anndata_path,
'n_processors' = n_processors,
'normalization' = normalization,
'tmp_dir' = temp_folder,
'tmp_dir' = tmp_dir,
'output_path' = precomp_stats_output_path,
'hierarchy' = hierarchy
)
Expand Down Expand Up @@ -207,25 +205,25 @@ save_precomp_stats_to_uns = function(anndata_path, precomp_stats_output_path, mo
#'
#' @param precomp_stats_output_path Local file path to the generated or user provided precomputed_stats.h5 file.
#' @param n_processors Number of independent worker processes to spin up.
#' @param temp_folder Temporary directory for writing out the hierarchical files (the code will clean these up after itself).
#' @param tmp_dir Temporary directory for writing out the hierarchical files (the code will clean these up after itself).
#'
#' @return File path of the reference marker file.
#'
#' @keywords internal
run_reference_markers = function(precomp_stats_output_path, n_processors, temp_folder) {
run_reference_markers = function(precomp_stats_output_path, n_processors, tmp_dir) {
ref_markers_config <- list(
'n_processors' = n_processors,
'precomputed_path_list' = list(precomp_stats_output_path),
'output_dir' = temp_folder,
'tmp_dir' = temp_folder
'output_dir' = tmp_dir,
'tmp_dir' = tmp_dir
)

ref_markers_runner = cell_type_mapper$cli$reference_markers$ReferenceMarkerRunner(
args=c(),
input_data=ref_markers_config)
ref_markers_runner$run()

ref_markers_file_path = file.path(temp_folder, "reference_markers.h5")
ref_markers_file_path = file.path(tmp_dir, "reference_markers.h5")
return(ref_markers_file_path)
}

Expand All @@ -234,21 +232,21 @@ run_reference_markers = function(precomp_stats_output_path, n_processors, temp_f
#' @param anndata_path Local file path of the AIT reference taxonomy (h5ad file).
#' @param ref_markers_file_path Local file path to the generated reference_marker.h5 file.
#' @param n_processors Number of independent worker processes to spin up.
#' @param temp_folder Temporary directory for writing out the hierarchical files (the code will clean these up after itself).
#' @param tmp_dir Temporary directory for writing out the hierarchical files (the code will clean these up after itself).
#'
#' @return File path of the query markers file.
#'
#' @keywords internal
run_query_markers = function(anndata_path, ref_markers_file_path, n_processors, temp_folder) {
run_query_markers = function(anndata_path, ref_markers_file_path, n_processors, tmp_dir) {
query_markers_filename = paste0(paste0("query_markers_", format(Sys.time(), "%Y%m%d-%H%M%S")), ".json")
query_markers_output_path = file.path(temp_folder, query_markers_filename)
query_markers_output_path = file.path(tmp_dir, query_markers_filename)

query_markers_config <- list(
'query_path' = anndata_path,
'reference_marker_path_list' = list(ref_markers_file_path),
'n_processors' = n_processors,
'output_path' = query_markers_output_path,
'tmp_dir' = temp_folder
'tmp_dir' = tmp_dir
)

query_markers_runner = cell_type_mapper$cli$query_markers$QueryMarkerRunner(
Expand Down Expand Up @@ -281,11 +279,11 @@ save_query_markers_to_uns = function(AIT_anndata, query_markers_output_path) {
#' This function saves the AIT reference taxonomy to a temp folder as h5ad, if the provided file path is invalid.
#' @param AIT_anndata AIT reference taxonomy object.
#' @param anndata_path Local file path of the AIT reference taxonomy (h5ad file).
#' @param temp_folder Temporary directory for writing out temporary files (the code will clean these up after itself).
#' @param tmp_dir Temporary directory for writing out temporary files (the code will clean these up after itself).
#' @return Local file path to the AIT reference taxonomy h5ad file.
#'
#' @keywords internal
get_anndata_path = function(AIT_anndata, anndata_path, temp_folder) {
get_anndata_path = function(AIT_anndata, anndata_path, tmp_dir) {
if (is.null(anndata_path) || !file.exists(anndata_path)){
# Use AIT path stored in AIT.anndata$uns, if not null.
if (!is.null(AIT_anndata$uns$taxonomyDir) && !is.null(AIT_anndata$uns$title)){
Expand All @@ -296,7 +294,7 @@ get_anndata_path = function(AIT_anndata, anndata_path, temp_folder) {
print(paste0(paste("WARNING: INVALID FILE PATH, ERROR in AIT.anndata$uns taxonomyDir and taxonomyName:", anndata_path),
". Writing the AIT.anndata to temperary location, SAVE anndata or FIX path to OPTIMIZE this step."))
anndata_filename <- paste0(paste0("temp_anndata_", format(Sys.time(), "%Y%m%d-%H%M%S")), ".h5ad")
anndata_path <- file.path(temp_folder, anndata_filename)
anndata_path <- file.path(tmp_dir, anndata_filename)
AIT_anndata$write_h5ad(anndata_path)
}
}
Expand Down

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