plot_reduced_dim_scExp: Plot reduced dimensions (PCA, TSNE, UMAP)

In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Description

Plot reduced dimensions (PCA, TSNE, UMAP)

Usage

plot_reduced_dim_scExp(
  scExp,
  color_by = "sample_id",
  reduced_dim = c("PCA", "TSNE", "UMAP"),
  select_x = "Component_1",
  select_y = "Component_2"
)

Arguments

scExp	A SingleCellExperiment Object
color_by	Feature used for coloration
reduced_dim	Reduced Dimension used for plotting
select_x	Which variable to select for x axis
select_y	Which variable to select for y axis

Value

A ggplot geom_point plot of reduced dimension 2D reprensentation

Examples

data("scExp")
plot_reduced_dim_scExp(scExp, color_by = "sample_id")
plot_reduced_dim_scExp(scExp, color_by = "total_counts")
plot_reduced_dim_scExp(scExp, reduced_dim = "UMAP")

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.