plotReducedDimension: Plot reduced dimension space.

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Plot reduced dimension space.

Description

Plot reduced dimension space using pca, tsne, diffusion components, UMAP or custom.

Usage

plotReducedDimension(
  object,
  assay.type = "RNA",
  reduction.type = c("tsne", "pca", "DC", "umap", "custom"),
  dims.use = c(1, 2),
  annotation,
  annotation.color,
  showlabels,
  dotsize = 1,
  labelsize = 3,
  convex = FALSE,
  percentage = 0.8,
  alpha = 0.1
)

Arguments

object	CellRouter object.
assay.type	character; the type of data to use.
reduction.type	character; the dimension reduction space to be used: pca, tsne, DC of diffusion components, umap, or custom.
dims.use	numeric vector; dimensions to use.
annotation	character; column in the metadata table to annotate the figure.
annotation.color	character; corresponding color column for the annotation.
showlabels	logical; show labels in the plot.
dotsize	numeric; dot size.
labelsize	numeric; label size.
convex	boolean; whether to connect the dots.
percentage	numeric; proportion of data in the panel (between 0 and 1).
alpha	numeric; transparency (between 0 and 1).

Value

ggplot2; plot.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.