In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

A total of r sum(metadata$doubletfinder_params$singlets_found, metadata$doubletfinder_params$multiplets_found) cells which passed QC were submitted to the multiplet identification algorithm "r metadata$scflow_steps$singlets_method". This identified r metadata$doubletfinder_params$multiplets_found multiplets and r metadata$doubletfinder_params$singlets_found singlets. To identify these, the variable(s) "r paste(metadata$doubletfinder_params$vars_to_regress_out, collapse = ", ")" were first regressed out of the data. The first r metadata$doubletfinder_params$pca_dims principal components were used to identify the r metadata$doubletfinder_params$var_features most variable genes. An assumed doublet formation rate of r metadata$doubletfinder_params$doublet_rate (i.e. r sprintf("%1.2f%%", metadata$doubletfinder_params$doublet_rate * 100) ) was applied.

Parameter sweep for optimal pK

r if(!metadata$doubletfinder_params$doubletfinder_sweep){sprintf("A pK value of %s was specified, therefore a parameter sweep was not performed.", metadata$doubletfinder_params$pK)}

knitr::opts_chunk$set(echo = FALSE)
metadata$qc_plots$doublet_finder$param_sweep

Multiplet visualization in two-dimensional space

The r metadata$doubletfinder_params$multiplets_found multiplets identified by "r metadata$scflow_steps$singlets_method" are visualized below in red in PCA space, tSNE space, and UMAP space.

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combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.