Dimension estimate diagnostic plot

Usage

DimsEstimatePlot(
  srt,
  max_pcs = 50,
  variance_thresholds = c(0.6, 0.7, 0.8, 0.9),
  reduction = NULL,
  palette = "Chinese",
  palcolor = NULL,
  aspect.ratio = NULL,
  title = NULL,
  subtitle = NULL,
  xlab = "Principal component",
  theme_use = "theme_scop",
  theme_args = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  seed = 11
)

Arguments

srt: A Seurat object with a PCA-like reduction computed.
max_pcs: Maximum number of PCs to visualize. Default is 50.
variance_thresholds: Numeric vector of variance thresholds to mark. Default is c(0.60, 0.70, 0.80, 0.90).
reduction: Reduction name to inspect. Default is NULL, which automatically selects a PCA-like reduction via DefaultReduction() with pattern = "pca".
palette: Palette used for the main curves. Default is "Chinese".
palcolor: Optional palette colors.
aspect.ratio: Aspect ratio of each panel. Default is NULL.
title: Title for the combined plot. When NULL (default), an auto-generated summary line is used.
subtitle: Subtitle for the combined plot. Default is NULL.
xlab: X-axis label shared by all panels. Default is "Principal component".
theme_use: Theme function used to style the plot. Default is "theme_scop".
theme_args: Other arguments passed to the theme_use.
combine: Whether to combine the four panels into one plot. Default is TRUE. When FALSE, returns a named list of ggplot objects.
nrow: Number of rows in the combined layout. Default is NULL.
ncol: Number of columns in the combined layout. Default is NULL
seed: Random seed. Default is 11.

Value

A patchwork plot object when combine = TRUE, or a named list of ggplot objects when combine = FALSE.