From 44a021068280f230ea1fc669f1b43574ea1d1d83 Mon Sep 17 00:00:00 2001 From: CBH Date: Sat, 5 Dec 2020 19:10:15 +0800 Subject: [PATCH 1/4] Update AnnotationGenome.R --- R/AnnotationGenome.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/AnnotationGenome.R b/R/AnnotationGenome.R index d35fa9ba..c61b8bb8 100644 --- a/R/AnnotationGenome.R +++ b/R/AnnotationGenome.R @@ -41,7 +41,7 @@ createGenomeAnnotation <- function( ################## message("Getting blacklist..") - blacklist <- .getBlacklist(genome = bsg@provider_version) + blacklist <- .getBlacklist(genome = bsg@metadata$genome) }else{ From 93339fd2ace1851bea0f66d5515db5b5346e2d6e Mon Sep 17 00:00:00 2001 From: CBH Date: Sat, 5 Dec 2020 19:12:22 +0800 Subject: [PATCH 2/4] Update AnnotationPeaks.R --- R/AnnotationPeaks.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/AnnotationPeaks.R b/R/AnnotationPeaks.R index 60b30642..04913b54 100644 --- a/R/AnnotationPeaks.R +++ b/R/AnnotationPeaks.R @@ -606,7 +606,7 @@ addArchRAnnotations <- function( } } - genome <- tolower(validBSgenome(getGenome(ArchRProj))@provider_version) + genome <- tolower(validBSgenome(getGenome(ArchRProj))@metadata$genome) annoPath <- file.path(find.package("ArchR", NULL, quiet = TRUE), "data", "Annotations") dir.create(annoPath, showWarnings = FALSE) From b91459f984b2a7b4e15664f96a93e45443533965 Mon Sep 17 00:00:00 2001 From: CBH Date: Wed, 9 Dec 2020 13:46:36 +0800 Subject: [PATCH 3/4] Update Embedding.R --- R/Embedding.R | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/R/Embedding.R b/R/Embedding.R index ba59be35..6e44ec96 100644 --- a/R/Embedding.R +++ b/R/Embedding.R @@ -223,14 +223,14 @@ addUMAP <- function( for (i in seq_len(n_metrics)) { nn_tmpfname <- file.path(uwot_dir, paste0("nn", i)) if (n_metrics == 1) { - model$nn_index$save(nn_tmpfname) + model$nn_index$ann$save(nn_tmpfname) model$nn_index$unload() - model$nn_index$load(nn_tmpfname) + model$nn_index$ann$load(nn_tmpfname) } else { - model$nn_index[[i]]$save(nn_tmpfname) + model$nn_index[[i]]$ann$save(nn_tmpfname) model$nn_index[[i]]$unload() - model$nn_index[[i]]$load(nn_tmpfname) + model$nn_index[[i]]$ann$load(nn_tmpfname) } } setwd(mod_dir) From 0b44a3ddd016b201124b8dc785275d27766941e0 Mon Sep 17 00:00:00 2001 From: CBH Date: Wed, 9 Dec 2020 13:54:41 +0800 Subject: [PATCH 4/4] Update Embedding.R --- R/Embedding.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/Embedding.R b/R/Embedding.R index 6e44ec96..80b4cf1a 100644 --- a/R/Embedding.R +++ b/R/Embedding.R @@ -224,12 +224,12 @@ addUMAP <- function( nn_tmpfname <- file.path(uwot_dir, paste0("nn", i)) if (n_metrics == 1) { model$nn_index$ann$save(nn_tmpfname) - model$nn_index$unload() + model$nn_index$ann$unload() model$nn_index$ann$load(nn_tmpfname) } else { model$nn_index[[i]]$ann$save(nn_tmpfname) - model$nn_index[[i]]$unload() + model$nn_index[[i]]$ann$unload() model$nn_index[[i]]$ann$load(nn_tmpfname) } }