From 0c4d7918c71700701ce34c0d461355a6b401af5b Mon Sep 17 00:00:00 2001 From: SarahOuologuem Date: Thu, 14 Mar 2024 11:45:46 +0000 Subject: [PATCH] add spatial normalization info --- docs/usage/normalization_methods.md | 37 ++++++++++++++++++----------- 1 file changed, 23 insertions(+), 14 deletions(-) diff --git a/docs/usage/normalization_methods.md b/docs/usage/normalization_methods.md index 8f1c0cb7..a0d945f5 100644 --- a/docs/usage/normalization_methods.md +++ b/docs/usage/normalization_methods.md @@ -2,7 +2,7 @@ Normalization methods ======================= -panpipes currently supports the following normalization methods: +`panpipes` currently supports the following normalization methods: ## RNA @@ -16,9 +16,9 @@ Additionally, the normalized data can be scaled using scanpy's [sc.pp.scale](htt 1. clr margin= 0, normalize within each cells' counts distribution, across all features (row-wise, as you would do for RNA data) 2. clr margin= 1, normalize within each feature's distribution, across all cells (column-wise, recommended for proteomics data) - *if you come from R, please note that the [margins are transposed](https://images.hindustantimes.com/rf/image_size_630x354/HT/p2/2017/09/21/Pictures/_78c6a162-9e94-11e7-9c3b-8e901839ece0.JPG) in the Python and anndata world* - - + *If you come from R, please note that the [margins are transposed](https://images.hindustantimes.com/rf/image_size_630x354/HT/p2/2017/09/21/Pictures/_78c6a162-9e94-11e7-9c3b-8e901839ece0.JPG) in the Python and anndata world.* + + 2. dsb using [muon's prot processing](https://muon.readthedocs.io/en/latest/api/generated/muon.prot.pp.html). This method is only applicable when you have raw 10x inputs (see [supported input files](https://panpipes-pipelines.readthedocs.io/en/latest/usage/setup_for_qc_mm.html#supported-input-filetypes)). @@ -31,6 +31,13 @@ Additionally, the normalized data can be scaled using scanpy's [sc.pp.scale](htt 2. "logTF": logging the TF term using using [muon's atac processing](https://muon.readthedocs.io/en/latest/api/generated/muon.atac.pp.tfidf.html#muon.atac.pp.tfidf) 3. "logIDF": logging the IDF term using using [muon's atac processing](https://muon.readthedocs.io/en/latest/api/generated/muon.atac.pp.tfidf.html#muon.atac.pp.tfidf) +## Spatial Transcriptomics + +1. Standard normalization using scanpy's [normalize_total](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.normalize_total.html) and [log1p](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.log1p.html). + +2. Analytic Pearson Residual normalization using scanpy's [normalize_pearson_residuals](https://scanpy.readthedocs.io/en/stable/generated/scanpy.experimental.pp.normalize_pearson_residuals.html). + + ## Layers nomenclature within each modality Raw, Normalised and Scaled data are saved for each modality in their specific layers: @@ -39,13 +46,15 @@ Raw, Normalised and Scaled data are saved for each modality in their specific la Using the following nomenclature: -| method | layer | modality | -| ---------------------- | --------------- | ------------- | -| raw counts | "raw_counts" | RNA/ATAC/PROT | -| standard log1p | "logged_counts" | RNA or ATAC | -| scaled counts | "scaled_counts" | RNA or ATAC | -| clr | "clr" | PROT | -| dsb | "dsb" | PROT | -| TFIDF (signac flavour) | "signac_norm" | ATAC | -| TFIDF (logTF) | "logTF_norm" | ATAC | -| TFIDF (logIDF) | "logIDF_norm" | ATAC | +| method | layer | modality | +| ---------------------- | -------------------- | ------------- | +| raw counts | "raw_counts" | RNA/ATAC/PROT | +| standard log1p | "logged_counts" | RNA or ATAC | +| scaled counts | "scaled_counts" | RNA or ATAC | +| clr | "clr" | PROT | +| dsb | "dsb" | PROT | +| TFIDF (signac flavour) | "signac_norm" | ATAC | +| TFIDF (logTF) | "logTF_norm" | ATAC | +| TFIDF (logIDF) | "logIDF_norm" | ATAC | +| standard log1p | "lognorm" | Spatial | +| Pearson Residuals | "norm_pearson_resid" | Spatial |