From a3379879177d1a832f912f4ff42980be7caea07a Mon Sep 17 00:00:00 2001 From: Luke Zappia Date: Mon, 20 Jan 2025 15:22:01 +0100 Subject: [PATCH 1/2] Replace "+" in batch names for liger --- src/methods/liger/script.R | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/methods/liger/script.R b/src/methods/liger/script.R index e5b7e451..a708e6d1 100644 --- a/src/methods/liger/script.R +++ b/src/methods/liger/script.R @@ -14,6 +14,7 @@ meta <- list( cat("Read input\n") adata <- anndata::read_h5ad(par$input) +adata$obs["batch"] <- sub("\\+", "plus", adata$obs[["batch"]]) # Replace "+"" characters in batch names anndataToLiger <- function(adata) { # fetch batch names @@ -30,7 +31,9 @@ anndataToLiger <- function(adata) { } addNormalizedDataToLiger <- function(adata, lobj) { + norm_data <- lapply(names(rliger::rawData(lobj)), function(name) { + norm <- adata$layers[["normalized"]] # subset From 07a38acfccec042af9bd4ce2d3eaa0cc6607c936 Mon Sep 17 00:00:00 2001 From: Luke Zappia Date: Mon, 20 Jan 2025 15:24:31 +0100 Subject: [PATCH 2/2] Undo extra lines --- src/methods/liger/script.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/methods/liger/script.R b/src/methods/liger/script.R index a708e6d1..1f77ca64 100644 --- a/src/methods/liger/script.R +++ b/src/methods/liger/script.R @@ -31,9 +31,7 @@ anndataToLiger <- function(adata) { } addNormalizedDataToLiger <- function(adata, lobj) { - norm_data <- lapply(names(rliger::rawData(lobj)), function(name) { - norm <- adata$layers[["normalized"]] # subset