umap: Create a umap plot; wrapper function for umap package plus...

In compbiomed/BatchQC: Batch Effects Quality Control Software

Create a umap plot; wrapper function for umap package plus custom plotting

Description

Create a umap plot; wrapper function for umap package plus custom plotting

Usage

umap(
  se_object,
  assay_of_interest,
  batch,
  neighbors = 15,
  min_distance = 0.1,
  spread = 1,
  exploratory = FALSE
)

Arguments

se_object	se_object; containing data of interest
assay_of_interest	string; the assay in the se_object to plot
batch	string; representing batch
neighbors	integer; number of nearest neighbors, default 15 per umap; lower values prioritize local structure, higher values will represent bigger picture but lose finer details
min_distance	numeric; how close points appear in final layout; higher values puts less emphasis on global structure; must be less than spread
spread	numeric; dispersion of points in umap
exploratory	Boolean; default is FALSE, if True, a 5x5 grid with k = 15, 25, 50, 100 and min_distance = 0.1, .2, .5, .75, .99 will be plotted

Value

umap plot

Examples

library(scran)
se <- mockSCE()
se$Treatment <- as.factor(se$Treatment)
se$Mutation_Status <- as.factor(se$Mutation_Status)
umap_plot <- BatchQC::umap(se_object = se, assay_of_interest = "counts",
batch = "Treatment")
umap_plot

compbiomed/BatchQC documentation built on June 10, 2025, 8:32 p.m.