transform/normalize_total

Description

Normalize counts per cell.

Normalize each cell by total counts over all genes, so that every cell has the same total count after normalization. If choosing target_sum=1e6, this is CPM normalization.

If exclude_highly_expressed=True, very highly expressed genes are excluded from the computation of the normalization factor (size factor) for each cell. This is meaningful as these can strongly influence the resulting normalized values for all other genes [Weinreb17].

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
output: "$id.$key.output"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/transform/normalize_total/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--modality	string	Which modality from the input MuData file to process.
--input_layer	string	Input layer to use. By default, X is normalized
--output -o	file required output	Output h5mu file.
--output_layer	string	Output layer to use. By default, use X.
--target_sum	integer	If None, after normalization, each observation (cell) has a total count equal to the median of total counts for observations (cells) before normalization.
--exclude_highly_expressed	boolean_true	Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell. A gene is considered highly expressed, if it has more than max_fraction of the total counts in at least one cell. The not-excluded genes will sum up to target_sum.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata H5 files. By default no compression is applied.

Name

Type & Properties

--input

-i

file

required

--modality

string

--input_layer

string

--output

-o

file

required

output

--output_layer

string

--target_sum

integer

--exclude_highly_expressed

boolean_true

--output_compression

string