plot_reduced_dim_scExp {ChromSCape}R Documentation

Plot reduced dimensions (PCA, TSNE, UMAP)

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")


[Package ChromSCape version 1.0.0 Index]