make_pca_selected_pcs_plot: Make a plot showing numbers of selected PCs from all...

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Make a plot showing numbers of selected PCs from all strategies.

Description

Make a plot showing numbers of selected PCs from all strategies.

Usage

make_pca_selected_pcs_plot(
  pca_percent_var,
  pca_elbow_pcs,
  pca_gene_var_pcs,
  pca_forced_pcs
)

Arguments

pca_percent_var	The percentage of variance explained by each PC. Obtained from attr(reducedDim(sce_pca, "pca"), "percentVar").
pca_elbow_pcs	A numeric scalar: number of PCs selected by elbow point strategy.
pca_gene_var_pcs	A numeric scalar: number of PCs selected by technical noise strategy.
pca_forced_pcs	A numeric scalar: constant number of PCs defined in config file.

Value

A ggplot object.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.