PlotUmap: Perform UMAP

In Galaxeee/TedSim: Temporal Dynamics Simulation of scRNA-seq and CRISR/Cas9 lineage barcodes

Perform UMAP

Description

This function takes the ground truth (meta), the expresssion matrix (data), and performs UMAP, saves the result to a jpeg file with user specified name

Usage

PlotUmap(
  meta,
  data,
  pca = T,
  n_pc,
  min_dist = 0.5,
  n_neighbors = 30,
  label,
  saving = F,
  plotname,
  system.color = T
)

Arguments

meta	simulation parameters
data	expression matrix
min_dist	minimum distance to identify neighborhood,default is 0.5
n_neighbors	The size of local neighborhood for manifold learning, default is 30
label	the column name of the meta data that the points needs to be colored by
plotname	the name of the jpeg file

Galaxeee/TedSim documentation built on Oct. 2, 2022, 1:25 a.m.