plot_umap — plot_umap • scMuffin

Generate a UMAP visualization

Usage

plot_umap(
  Seu_obj,
  file = "umap.jpg",
  labels = NULL,
  group.by = NULL,
  feature_plot = FALSE,
  lab_size = 1,
  lab_color = "black",
  adj_outliers = FALSE,
  width = 180,
  height = 180,
  units = "mm",
  res = 300,
  text.size = 5,
  ...
)

Arguments

Seu_obj: seurat object, object with saved dimension reduction components
file: string, file name output
labels: cluster labels
group.by: a feature to colour by (e.g. cluster ID)
feature_plot: whether to call Seurat::FeaturePlot
lab_size: label size
lab_color: label color
adj_outliers: logical, whether to adjust the group.by scores, removing outliers
width: image width
height: image height
units: image units
res: image resolution
text.size: text size
...: further arguments for Seurat::FeaturePlot or Seurat::DimPlot

Details

Generate a UMAP visualization