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Use template for docs
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@mojaveazure
mojaveazure committed May 23, 2023
1 parent 45e0ffc commit 75be023
Showing 1 changed file with 100 additions and 86 deletions.
186 changes: 100 additions & 86 deletions apis/r/R/SOMAExperimentAxisQuery.R
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Original file line number Diff line number Diff line change
Expand Up @@ -174,8 +174,7 @@ SOMAExperimentAxisQuery <- R6::R6Class(
#' @template param-x-layers-v3
#' @template param-obs-index
#' @template param-var-index
#' @param obs_column_names Names of columns in \code{obs} to add as
#' cell-level meta data; by default, loads all columns
#' @template param-obs-column-names
#' @template param-var-column-names
#' @param obsm_layers Names of arrays in \code{obsm} to load in as the
#' cell embeddings; pass \code{FALSE} to suppress loading in any
Expand Down Expand Up @@ -269,79 +268,88 @@ SOMAExperimentAxisQuery <- R6::R6Class(
skip_reducs <- TRUE
}
if (!skip_reducs) {
names(ms_embed) <- .anndata_to_seurat_reduc(ms_embed)
if (isTRUE(obsm_layers)) {
obsm_layers <- NULL
}
obsm_layers <- obsm_layers %||% ms_embed
# Match loadings to embeddings
ms_load <- tryCatch(expr = self$ms$varm$names(), error = null)
if (isTRUE(varm_layers)) {
varm_layers <- NULL
} else if (rlang::is_na(varm_layers)) {
varm_layers <- FALSE
}
if (is.null(ms_load)) {
if (!(isFALSE(varm_layers) || is.null(varm_layers))) {
warning("No loadings found", call. = FALSE, immediate. = TRUE)
}
varm_layers <- FALSE
}
if (!isFALSE(varm_layers)) {
names(ms_load) <- ms_embed[.anndata_to_seurat_reduc(ms_load, 'loadings')]
varm_layers <- varm_layers %||% ms_load
reduc_misisng <- setdiff(x = names(varm_layers), y = names(ms_load))
if (length(reduc_misisng) == length(varm_layers)) {
warning(
"None of the reductions specified in 'varm_layers' can be found",
call. = FALSE,
immediate. = TRUE
)
varm_layers <- FALSE
} else if (length(reduc_misisng)) {
warning(
paste(
strwrap(paste(
"The reductions for the following loadings cannot be found in 'varm':",
sQuote(varm_layers[reduc_misisng]),
collapse = ', '
)),
collapse = '\n'
),
call. = FALSE,
immediate. = TRUE
)
varm_layers <- varm_layers[!names(varm_layers) %in% reduc_misisng]
}
}
# Read in reductions and add to `object`
for (embed in obsm_layers) {
if (embed %in% names(ms_embed)) {
embed <- ms_embed[embed]
# obsm_layers <- obsm_layers %||% ms_embed
# # Match loadings to embeddings
# ms_load <- tryCatch(expr = self$ms$varm$names(), error = null)
# if (isTRUE(varm_layers)) {
# varm_layers <- NULL
# } else if (rlang::is_na(varm_layers)) {
# varm_layers <- FALSE
# }
# if (is.null(ms_load)) {
# if (!(isFALSE(varm_layers) || is.null(varm_layers))) {
# warning("No loadings found", call. = FALSE, immediate. = TRUE)
# }
# varm_layers <- FALSE
# }
# if (!isFALSE(varm_layers)) {
# names(ms_load) <- ms_embed[.anndata_to_seurat_reduc(ms_load, 'loadings')]
# varm_layers <- varm_layers %||% ms_load
# reduc_misisng <- setdiff(x = names(varm_layers), y = names(ms_load))
# if (length(reduc_misisng) == length(varm_layers)) {
# warning(
# "None of the reductions specified in 'varm_layers' can be found",
# call. = FALSE,
# immediate. = TRUE
# )
# varm_layers <- FALSE
# } else if (length(reduc_misisng)) {
# warning(
# paste(
# strwrap(paste(
# "The reductions for the following loadings cannot be found in 'varm':",
# sQuote(varm_layers[reduc_misisng]),
# collapse = ', '
# )),
# collapse = '\n'
# ),
# call. = FALSE,
# immediate. = TRUE
# )
# varm_layers <- varm_layers[!names(varm_layers) %in% reduc_misisng]
reductions <- tryCatch(
expr = .get_seurat_reductions(
query = self,
obsm_layers = obsm_layers,
varm_layers = varm_layers,
obs_index = obs_index,
var_index = var_index
),
error = function(e) {
warning(conditionMessage(e), call. = FALSE, immediate. = TRUE)
return(NULL)
}
rname <- .anndata_to_seurat_reduc(embed)
reduc <- withCallingHandlers(
expr = tryCatch(
expr = self$to_seurat_reduction(
obsm_layer = embed,
varm_layer = ifelse(
embed %in% names(varm_layers),
yes = varm_layers[embed],
no = FALSE
),
obs_index = obs_index,
var_index = var_index
),
error = err_to_warn
),
noArrayWarning = function(w) {
invokeRestart("muffleWarning")
}
)
if (!inherits(reduc, 'DimReduc')) {
next
)
if (length(reductions)) {
for (reduc in names(reductions)) {
object[[reduc]] <- reductions[[reduc]]
}
object[[rname]] <- reduc
# rname <- .anndata_to_seurat_reduc(embed)
# reduc <- withCallingHandlers(
# expr = tryCatch(
# expr = self$to_seurat_reduction(
# obsm_layer = embed,
# varm_layer = ifelse(
# embed %in% names(varm_layers),
# yes = varm_layers[embed],
# no = FALSE
# ),
# obs_index = obs_index,
# var_index = var_index
# ),
# error = err_to_warn
# ),
# noArrayWarning = function(w) {
# invokeRestart("muffleWarning")
# }
# )
# if (!inherits(reduc, 'DimReduc')) {
# next
# }
# object[[rname]] <- reduc
}
}
# Load in graphs
Expand All @@ -357,21 +365,28 @@ SOMAExperimentAxisQuery <- R6::R6Class(
if (isTRUE(obsp_layers)) {
obsp_layers <- NULL
}
obsp_layers <- obsp_layers %||% ms_graphs
for (grph in obsp_layers) {
mat <- withCallingHandlers(
expr = tryCatch(
expr = self$to_seurat_graph(obsp_layer = grph, obs_index = obs_index),
error = err_to_warn
),
noArrayWarning = function(w) {
invokeRestart("muffleWarning")
}
)
if (!inherits(mat, 'Graph')) {
next
# obsp_layers <- obsp_layers %||% ms_graphs
# for (grph in obsp_layers) {
# mat <- withCallingHandlers(
# expr = tryCatch(
# expr = self$to_seurat_graph(obsp_layer = grph, obs_index = obs_index),
# error = err_to_warn
# ),
# noArrayWarning = function(w) {
# invokeRestart("muffleWarning")
# }
# )
# if (!inherits(mat, 'Graph')) {
# next
graphs <- .get_seurat_graphs(
query = self,
obsp_layers = obsp_layers,
obs_index = obs_index
)
if (length(graphs)) {
for (grph in names(graphs)) {
object[[grph]] <- graphs[[grph]]
}
object[[grph]] <- mat
}
}
# Validate and return
Expand Down Expand Up @@ -651,8 +666,7 @@ SOMAExperimentAxisQuery <- R6::R6Class(
)),
collapse = '\n'
),
call. = FALSE,
immediate. = TRUE
call. = FALSE
)
loads$read_dense_matrix(unname(coords))
} else {
Expand Down

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