seurat_plot_dimred_counts: DimensionReduction with counts plot

View source: R/plot_dimred_counts.R

seurat_plot_dimred_countsR Documentation

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.