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adding seurat clusters & annotations fixed #33

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Apr 7, 2021
Merged

adding seurat clusters & annotations fixed #33

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33 changes: 18 additions & 15 deletions R/loom.R
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Original file line number Diff line number Diff line change
Expand Up @@ -431,7 +431,7 @@ add_global_md_clustering_kv <- function(
) == clustering.id

if(sum(mask) == 0) {
stop("Cannot add key/value to clustering that do not exists.")
stop("Cannot add key/value to clustering that does not exist.")
}
idx <- which(mask == T)

Expand Down Expand Up @@ -540,6 +540,9 @@ update_cluster_descriptions_by_cluster_annotation_mapping_df <- function(
in.place = TRUE
) {
if(loom$mode=="r") stop("File open as read-only.")

## make sure annotation.df cluster id column is numeric!
annotation.df[, annotation.df.cluster.id.column.name] <- as.numeric(annotation.df[, annotation.df.cluster.id.column.name])

gmd <- get_global_meta_data(loom = loom)
gmd_clusterings <- gmd[[GA_METADATA_CLUSTERINGS_NAME]]
Expand Down Expand Up @@ -572,8 +575,8 @@ update_cluster_descriptions_by_cluster_annotation_mapping_df <- function(
if(!(annotation.df.annotation.column.name %in% colnames(x = annotation.df))) {
stop(paste0("The given '",annotation.df.annotation.column.name,"' does not exist in the given annotation.df."))
}
annotation_names <- annotation[[annotation.df.annotation.column.name]]
cluster_ids <- annotation[[annotation.df.cluster.id.column.name]]
annotation_names <- annotation.df[[annotation.df.annotation.column.name]]
cluster_ids <- annotation.df[[annotation.df.cluster.id.column.name]]
annotation_as_named_list <- setNames(
object = annotation_names,
nm = cluster_ids
Expand All @@ -588,7 +591,7 @@ update_cluster_descriptions_by_cluster_annotation_mapping_df <- function(
if(!reset) {
# If annotation for the current cluster not empty then add
# Convert from factor to character vector to be used with nchar
d <- as.character(x = annotation_as_named_list[cluster.id])
d <- as.character(x = annotation_as_named_list[as.character(cluster.id)])

if(length(d) > 1) {
stop("Annotation is not unique: multiple annotation correspond to a cluster ID.")
Expand Down Expand Up @@ -1000,6 +1003,7 @@ add_embedding <- function(
key = CA_EXTRA_EMBEDDINGS_NAMES[i]
)
e <- as.data.frame(x = embedding[,i])
id <- as.character(x = ncol(x = ca.embeddings))
colnames(x = e) <- id
ca.embeddings <- cbind(ca.embeddings, e)
# Update the current coordinates Embeddings
Expand Down Expand Up @@ -1149,13 +1153,13 @@ get_unique_clusters <- function(
if(is.factor(x = clusters)) {
return (
sort(
x = levels(x = clusters),
x = as.numeric(levels(x = clusters)),
decreasing = F)
)
} else {
return (
sort(
x = unique(x = clusters),
x = as.numeric(unique(x = clusters)),
decreasing = F
)
)
Expand Down Expand Up @@ -1217,8 +1221,8 @@ get_seurat_clustering_resolutions <- function(
#'@param loom The loom file handler.
#'@param seurat The Seurat object
#'@param seurat.assay The assay to access the data from (only if you're using Seurat version 3). Option used only for sanity checks.
#'@param seurat.markers.file.path.list The named list of file paths to the markers saved in RDS format. The names should be the resolution id of the corresponding clustering (e.g.: res.2). Default is NULL.
#'@param default.clustering.resolution The clustering resolution (i.e.: res.2, ...) of the clustering that should be set as the default which an annotation can be set for.
#'@param seurat.markers.file.path.list The named list of file paths to the markers saved in RDS format. The names should be the resolution id of the corresponding clustering (e.g.: SCT_snn_res.0.5). Default is NULL.
#'@param default.clustering.resolution The clustering resolution (i.e.: '0.5' or 'SCT_snn_res.0.5') of the clustering that should be set as the default which an annotation can be set for.
#'@param annotation A data.frame with annotation for the clusters of the default clustering. Default is NULL.
#'@param annotation.cluster.id.cn The column name to use for the IDs of the clusters found by the given clustering group. Default is NULL.
#'@param annotation.cluster.description.cn The column name to use for the description of the clusters found by the given clustering group. Default is NULL.
Expand Down Expand Up @@ -1429,7 +1433,7 @@ create_cluster_annotation <- function(
unique_clusters <- get_unique_clusters(clusters = clusters)
annotation <- setNames(
object = rep(NA, length(x = clusters)),
nm = names(x = clusters)
nm = names(clusters)
)

for(cluster.idx in seq_along(along.with = unique_clusters)) {
Expand All @@ -1443,14 +1447,13 @@ create_cluster_annotation <- function(
}
if(!is.null(x = cluster.meta.data.df)) {
if(!(cluster.description.cn %in% colnames(x = cluster.meta.data.df))) {
stop(paste0("The given column ",cluster.description.cn, " does not exists in the annotation provided."))
stop(paste0("The given column ",cluster.description.cn, " does not exist in the annotation provided."))
}
description <- as.vector(x = unlist(x = cluster.meta.data.df[cluster.meta.data.df[[cluster.id.cn]] == cluster, cluster.description.cn]))
description <- as.vector(x = unlist(x = cluster.meta.data.df[cluster.meta.data.df[[cluster.id.cn]] == cluster_id, cluster.description.cn]))
}
annotation[as.vector(x = unlist(x = clusters)) == cluster_id] <- description
}
annotation <- factor(x = annotation)
names(x = annotation) <- names(x = clusters)
return (annotation)
}

Expand Down Expand Up @@ -1631,7 +1634,7 @@ add_annotated_clustering <- function(
}
# Adding the clustering data
if(col_attrs_exists_by_key(loom = loom, key = CA_CLUSTERINGS_NAME)) {
print(paste(CA_CLUSTERINGS_NAME, "already exists..."))
print(paste0("col_attr '", CA_CLUSTERINGS_NAME, "' already exists..."))
ca_clusterings <- get_clusterings(loom = loom)
# Set the clustering id
id <- ncol(x = ca_clusterings) # n clusterings (start at 0)
Expand Down Expand Up @@ -1669,7 +1672,7 @@ add_annotated_clustering <- function(
annotation = annotation
)
flush(loom = loom)
return (id)
return(id)
}

#*******************#
Expand Down Expand Up @@ -2920,7 +2923,7 @@ get_cell_ids <- function(
is.flybase.gn = F
) {
ra <- loom[["col_attrs"]]
return (ra[[CA_CELLID]][])
return(ra[[CA_CELLID]][])
}

#'@title get_genes
Expand Down