From 9dd67b1a65950675bb81671a30bf7beb026c0856 Mon Sep 17 00:00:00 2001
From: Wojciech Lason <40389067+wlason@users.noreply.github.com>
Date: Fri, 26 Jul 2024 13:08:23 +0200
Subject: [PATCH] Update multimodal integration documentation
Removed typos.
Corrected how to specify method names (list not string) and updated how they are spelled (e.g. MOFA is mofa, TotalVI is totalvi).
---
docs/yaml_docs/pipeline_integration_yml.md | 17 ++++++++++++-----
1 file changed, 12 insertions(+), 5 deletions(-)
diff --git a/docs/yaml_docs/pipeline_integration_yml.md b/docs/yaml_docs/pipeline_integration_yml.md
index 76c8e899..bb31f119 100644
--- a/docs/yaml_docs/pipeline_integration_yml.md
+++ b/docs/yaml_docs/pipeline_integration_yml.md
@@ -279,14 +279,21 @@ For more information on `bbknn` check the [bbknn documentation](https://bbknn.re
- run `Boolean`, Default: True
Set to False if you don't want to run multimodal integration
- - tools `String`(Comma separated), Default: "WNN"
- Method you want to use to run batch correction. Options include: WNN, totalvi and multiVI. You can specify mutiple methods and they will be run simultaneously.
+ - tools `String`(list), Default: "WNN"
+ Method you want to use to run batch correction. Options include:
+ - methods with set modalities: totalVI (rna, prot) and multiVI (rna, atac)
+ - totalvi
+ - MultiVI
+ - methods which accept any combination of modalities: MOFA and WNN
+ - mofa
+ - WNN
+
+ You can specify mutiple methods and they will be run simultaneously.
+ It makes biological sense to include rna modality if available, which is most informative in terms of cell type differences.
- column_categorical `String`(Comma separated), Default: sample_id
This is the column you want to run a batch correction on.
- Mltiple columns can be selected simultaneously by providing them as a comma-separated string without spaces.
-
- Extra parameters:
+ Multiple columns can be selected simultaneously by providing them as a comma-separated string without spaces.
### TotalVI arguments