From 50437149052efa9f3c3c65c0042e1da2dc9ea223 Mon Sep 17 00:00:00 2001 From: Lilly Date: Wed, 6 Mar 2024 10:35:39 +0100 Subject: [PATCH] Set default clr margin to 1 --- docs/yaml_docs/pipeline_preprocess_yml.md | 4 ++-- panpipes/panpipes/pipeline_preprocess/pipeline.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/yaml_docs/pipeline_preprocess_yml.md b/docs/yaml_docs/pipeline_preprocess_yml.md index 168a940b..cd9cab75 100644 --- a/docs/yaml_docs/pipeline_preprocess_yml.md +++ b/docs/yaml_docs/pipeline_preprocess_yml.md @@ -325,10 +325,10 @@ Whether applying scaling or not is still a matter of debate, as stated in the [L If you choose to run both (dsb and clr), then 'dsb' is stored in X as default. For downstream visualisation, you can either specify the layer, or take the default stored in X. - - clr_margin `Integer` (0 or 1), Default: 0
+ - clr_margin `Integer` (0 or 1), Default: 1
Parameter for CLR normalisation. The CLR margin determines whether you normalise per cell (as you would normalise RNA data), or by feature (recommended, due to the variable nature of protein assays). - Hence, CLR margin 0 is recommended for informative qc plots in this pipeline. + Hence, CLR margin 1 is recommended for informative qc plots in this pipeline. - 0 = normalise row-wise (per cell) - 1 = normalise column-wise (per feature) diff --git a/panpipes/panpipes/pipeline_preprocess/pipeline.yml b/panpipes/panpipes/pipeline_preprocess/pipeline.yml index 60bf6bed..11efe857 100644 --- a/panpipes/panpipes/pipeline_preprocess/pipeline.yml +++ b/panpipes/panpipes/pipeline_preprocess/pipeline.yml @@ -157,7 +157,7 @@ prot: # CLR parameters: # 0 = normalise row-wise (per cell) # 1 = normalise column-wise (per feature, recommended) - clr_margin: 0 + clr_margin: 1 # DSB parameters: background_obj: