qc/calculate_qc_metrics

Description

Add basic quality control metrics to an .h5mu file.

The metrics are comparable to what scanpy.pp.calculate_qc_metrics output,
although they have slightly different names:

Var metrics (name in this component -> name in scanpy):

pct_dropout -> pct_dropout_by_{expr_type}
num_nonzero_obs -> n_cells_by_{expr_type}
obs_mean -> mean_{expr_type}
total_counts -> total_{expr_type}

Obs metrics:
- num_nonzero_vars -> n_genes_by_{expr_type}
- pct_{var_qc_metrics} -> pct_{expr_type}{qc_var}
- total_counts{var_qc_metrics} -> total_{expr_type}{qc_var}
- pct_of_counts_in_top{top_n_vars}vars -> pct{expr_type}in_top{n}{var_type}
- total_counts -> total{expr_type}

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_obs_num_nonzero_vars: [ "num_nonzero_vars" ]  
output_obs_total_counts_vars: [ "total_counts" ]  
output_var_num_nonzero_obs: [ "num_nonzero_obs" ]  
output_var_total_counts_obs: [ "total_counts" ]  
output_var_obs_mean: [ "obs_mean" ]  
output_var_pct_dropout: [ "pct_dropout" ]  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.2 \  
  -main-script target/nextflow/qc/calculate_qc_metrics/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input h5mu file
--modality	string	Which modality from the input MuData file to process.
--layer	string	Layer from modality to use as input data. If not provided the .X attribute is used.

Name

Type & Properties

--input

file

required

--modality

string

--layer

string

Metrics added to .obs

Name	Type & Properties	Description
--var_qc_metrics	string multiple	Keys to select a boolean (containing only True or False) column from .var. For each cell, calculate the proportion of total values for genes which are labeled 'True', compared to the total sum of the values for all genes.
--var_qc_metrics_fill_na_value	boolean	Fill any 'NA' values found in the columns specified with --var_qc_metrics to 'True' or 'False'. as False.
--top_n_vars	integer multiple	Number of top vars to be used to calculate cumulative proportions. If not specified, proportions are not calculated. `--top_n_vars 20;50` finds cumulative proportion to the 20th and 50th most expressed vars.
--output_obs_num_nonzero_vars	string	Name of column in .obs describing, for each observation, the number of stored values (including explicit zeroes). In other words, the name of the column that counts for each row the number of columns that contain data.
--output_obs_total_counts_vars	string	Name of the column for .obs describing, for each observation (row), the sum of the stored values in the columns.

Name

Type & Properties

--var_qc_metrics

string

multiple

--var_qc_metrics_fill_na_value

boolean

--top_n_vars

integer

multiple

--output_obs_num_nonzero_vars

string

--output_obs_total_counts_vars

string

Metrics added to .var

Name	Type & Properties	Description
--output_var_num_nonzero_obs	string	Name of column describing, for each feature, the number of stored values (including explicit zeroes). In other words, the name of the column that counts for each column the number of rows that contain data.
--output_var_total_counts_obs	string	Name of the column in .var describing, for each feature (column), the sum of the stored values in the rows.
--output_var_obs_mean	string	Name of the column in .obs providing the mean of the values in each row.
--output_var_pct_dropout	string	Name of the column in .obs providing for each feature the percentage of observations the feature does not appear on (i.e. is missing). Same as `--num_nonzero_obs` but percentage based.

Name

Type & Properties

--output_var_num_nonzero_obs

string

--output_var_total_counts_obs

string

--output_var_obs_mean

string

--output_var_pct_dropout

string

Outputs

Name	Type & Properties	Description
--output	file output	Output h5mu file.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output

file

output

--output_compression

string