plot_embedding: Plot low-dimensional cell embedding

In OliverDietrich/SeuratHelper: Helper functions to assist scRNA-seq data analysis from a Seurat object

Plot low-dimensional cell embedding

Description

This function creates a plot of a cell embedding stored in a Seurat object. Cells can be colored by gene expression or metadata.

Usage

plot_embedding(
  object = NULL,
  color = "",
  split.by = NULL,
  label = FALSE,
  embedding = tail(names(object@reductions), 1),
  ann_colors = NULL,
  pt.aggr = TRUE,
  pt.aggr.breaks = 300,
  pt.size = 1,
  pt.stroke = 0.1,
  dim.1 = 1,
  dim.2 = 2,
  brush = NULL,
  cells = NULL,
  n.cells = NULL,
  assay = Seurat::DefaultAssay(object),
  slot = "data",
  theme.size = 15,
  label.size = 6,
  split.by.rows = NULL,
  split.by.max = 20,
  dict = object@misc$features,
  from = 1,
  to = 2,
  alpha = 1,
  shape = 20,
  color.transform = "",
  pl.title = NULL,
  legend.position = "right",
  legend.cols = NULL
)

Arguments

object	Seurat object
color	Gene or metadata to color cells
split.by	Metadata to split plot by
label	Type of group labels (text or label)
embedding	Name of the embedding (e.g. 'umap')
ann_colors	Named vector of annotation colors
pt.aggr	Whether to summarize overlapping points
pt.aggr.breaks	Number of breaks to summarize overlapping points. Less breaks result in a coarser image, summarizing more points.
pt.size	Point size
dim.1	Matrix column to use for x-axis
dim.2	Matrix column to use for y-axis
brush	Brushed points (xmin, xmax, ymin, ymax)
cells	Character of cell barcodes to plot
n.cells	Number of cells to plot (randomly sampled)
assay	Assay with expression data (e.g. RNA)
slot	Slot of expression data (counts, data, scale.data)
dict	Dictionary for the convert_features function
from	From argument for convert_features
to	To argument for convert_features
alpha	Transparency of points (0-1)
color.transform	Transformation of values used for color. Options include log, log2, log1p, log10
legend.position	Position of the color legend.

OliverDietrich/SeuratHelper documentation built on Jan. 20, 2024, 2:57 a.m.