seurat_plot_dimred_counts: DimensionReduction with counts plot

In Terkild/scutility: Utility Functions For Multi-modal Single-cell Analysis

DimensionReduction with counts plot

Description

Very crude and hardcoded function that calls Seurat::FeaturePlot. Needs a remake for more flexibility.

Usage

seurat_plot_dimred_counts(
  object,
  feature,
  split.by = NULL,
  colors = c("#000033", "#3377FF", "#33AAFF", "#33CC33", "orange", "red"),
  limits = c(0, NA),
  order = FALSE,
  slot = "counts",
  max.cutoff = "q95",
  pt.size = 0.75,
  legend.key.width = unit(5, "mm"),
  legend.key.height = unit(2, "mm"),
  legend.text = element_text(angle = 45),
  combine = TRUE,
  ...
)

Arguments

object	Seurat object
feature	Seurat feature
split.by	Meta.data column in seurat object for splitting
colors	Color palette
limits	Limits for color palette (for counts it makes sense that lower limit is 0; DEFAULT: c(0, NA))
order	Should cells be ordered by expression
slot	Seurat slot
max.cutoff	max.cutoff passed on to FeaturePlot
pt.size	pt.size passed on to FeaturePlot
legend.key.width	Theme settings for width of legend
legend.key.height	Theme settings for height of legend
legend.text	Theme settings for
combine	Should plots be combined or returned as a list of plots?
...	Passed on to Seurat::FeaturePlot

Value

ggplot2 object(s)

Terkild/scutility documentation built on Jan. 16, 2025, 5:28 p.m.