From 0d977ef584182d8c0c5e8cd19fce1034190c6e26 Mon Sep 17 00:00:00 2001 From: Lilly Date: Mon, 29 Apr 2024 23:33:30 +0200 Subject: [PATCH] Added docs parameter explanation --- docs/yaml_docs/pipeline_integration_yml.md | 17 +++++++++++++++++ .../panpipes/pipeline_integration/pipeline.yml | 1 + 2 files changed, 18 insertions(+) diff --git a/docs/yaml_docs/pipeline_integration_yml.md b/docs/yaml_docs/pipeline_integration_yml.md index a3dafb55..c2e6ef7c 100644 --- a/docs/yaml_docs/pipeline_integration_yml.md +++ b/docs/yaml_docs/pipeline_integration_yml.md @@ -436,6 +436,23 @@ Any metrics you may want to plot on all modality UMAPs should be listed under `a If you want to add any additional plots, simply remove the log file (logs/plot_batch_corrected_umaps.log) and run `panpipes integration make plot_umaps`. + +## scib metrics +To assess the unimodal data integration, we use the scib metrics. +The metrics are calculated using the `scib-metrics` package. +The metrics are calculated and stored for each modality separately. + +- scib:
+ - rna `String`, Optional
+ Obs column name for the rna modality containing the cell type labels. + If not provided, only a subset of the metrics working without cell type labels will be calculated. + Especially the bio conservation metrics will not be calculated, which also prevents creating the benchmarking plots. + - prot `String`, Optional
+ Obs column name for the prot modality containing the cell type labels. + - atac `String`, Optional
+ Obs column name for the atac modality containing the cell type labels. + + ## Creating the final object Leave this final option blank until you have reviewed the results from running `panpipes integration make full`. diff --git a/panpipes/panpipes/pipeline_integration/pipeline.yml b/panpipes/panpipes/pipeline_integration/pipeline.yml index f77eb337..794580be 100644 --- a/panpipes/panpipes/pipeline_integration/pipeline.yml +++ b/panpipes/panpipes/pipeline_integration/pipeline.yml @@ -244,6 +244,7 @@ plotqc: #------------- # scib metrics #------------- +#Obs columns containing the cell type labels scib: rna: prot: