diff --git a/docs/yaml_docs/spatial_preprocess.md b/docs/yaml_docs/spatial_preprocess.md index f9ff2605..1e2dac66 100644 --- a/docs/yaml_docs/spatial_preprocess.md +++ b/docs/yaml_docs/spatial_preprocess.md @@ -100,7 +100,7 @@ The parameters below specify which metrics of the filtered data to plot. As for ## 4. Normalization, HVG Selection, and PCA Options -### **4.1 Normalization and HVG Selection**
+### **4.1 Normalization and HVG Selection** `Panpipes` offers two different normalization and HVG selection flavours, `'seurat'` and `'squidpy'`.
The `'seurat'` flavour first selects HVGs on the raw counts using analytic Pearson residuals, i.e. [scanpy.experimental.pp.highly_variable_genes](https://scanpy.readthedocs.io/en/stable/generated/scanpy.experimental.pp.highly_variable_genes.html). Afterwards, analytic Pearson residual normalization is applied, i.e. [scanpy.experimental.pp.normalize_pearson_residuals](https://scanpy.readthedocs.io/en/stable/generated/scanpy.experimental.pp.normalize_pearson_residuals.html). Parameters of both functions can be specified by the user in the yaml file.
The `'squidpy'` flavour runs the basic scanpy normalization and HVG selection functions, i.e. [scanpy.pp.normalize_total](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.normalize_total.html), [scanpy.pp.log1p](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.log1p.html), and [scanpy.pp.highly_variable_genes](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.highly_variable_genes.html).
@@ -109,6 +109,7 @@ The parameters below specify which metrics of the filtered data to plot. As for
___Parameters for `norm_hvg_flavour` == `'squidpy'`___
+ squidpy_hvg_flavour[`'seurat'`,`'cellranger'`,`'seurat_v3'`], Default: 'seurat'
Flavour to select HVGs, i.e.`flavor` parameter of the function [scanpy.pp.highly_variable_genes](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.highly_variable_genes.html). @@ -122,6 +123,7 @@ ___Parameters for `norm_hvg_flavour` == `'squidpy'`___
Parameter in [scanpy.pp.highly_variable_genes](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.highly_variable_genes.html). ___Parameters for `norm_hvg_flavour` == `'seurat'`___
+ theta`Float`, Default: 100
The negative binomial overdispersion parameter for pearson residuals. The same value is used for [HVG selection]((https://scanpy.readthedocs.io/en/stable/generated/scanpy.experimental.pp.highly_variable_genes.html)) and [normalization](https://scanpy.readthedocs.io/en/stable/generated/scanpy.experimental.pp.normalize_pearson_residuals.html). @@ -129,6 +131,7 @@ ___Parameters for `norm_hvg_flavour` == `'seurat'`___
Specifies clipping of the residuals.
`clip` can be specified as:
___Parameters for both `norm_hvg_flavour` flavours___
+ n_top_genes`Integer`, Default: 2000
Number of genes to select. Mandatory for `norm_hvg_flavour='seurat'` and `squidpy_hvg_flavour='seurat_v3'`. diff --git a/docs/yaml_docs/spatial_qc.md b/docs/yaml_docs/spatial_qc.md index 5e4b1f49..a2795c53 100644 --- a/docs/yaml_docs/spatial_qc.md +++ b/docs/yaml_docs/spatial_qc.md @@ -74,7 +74,7 @@ This part of the workflow allows to generate additional QC metrics that can be u Comma-separated string without spaces, e.g. _mito,hp,rp_.
For which groups of the csv-file specified in `custom_genes_file` to run [scanpy.tl.score_genes](https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.score_genes.html)
-The following parameters specify the QC metrics to plot in violin and spatial embedding plots. Plots are generated for each slide specified in the submission file separately. +The following parameters specify the QC metrics to plot in violin and spatial embedding plots. Plots are generated for each slide specified in the submission file separately.

plotqc