Merge pull request #231 from DendrouLab/sarah_spatial_norm_info

Add spatial normalization info
DendrouLab · Mar 14, 2024 · c94a59b · c94a59b
2 parents c61e5cc + 0c4d791
commit c94a59b
Showing 1 changed file with 23 additions and 14 deletions.
diff --git 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*
-
-   <img src="https://github.com/DendrouLab/panpipes/tree/main/docs/img/clr_margins.png" width="65%">
+    *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.*
+    
+    <img src="../img/clr_margins.png" width="40%">
 
 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       |