UMAP Visualization colored by features — plot_umap_colored

Generate UMAP visualizations for all the columns in the "summary" element of a feature available in scMuffinList. For every column a png file is saved in out_dir. It requires a Seurat object with UMAP information.

Usage

plot_umap_colored_features(
  Seu_obj = NULL,
  scMuffinList = NULL,
  feature_name = NULL,
  scale_feature = FALSE,
  adj_outliers = FALSE,
  min_cells = 10,
  out_dir = "./",
  width = 180,
  height = 180,
  units = "mm",
  res = 300,
  ...
)

Arguments

Seu_obj: Seurat object with UMAP data
scMuffinList: scMuffinList object
feature_name: feature name
scale_feature: whether to scale feature values
adj_outliers: logical, whether to adjust the feature scores, removing outliers
min_cells: minimum number of cells in which the feature must have a non-zero value
out_dir: output directory
width: image width
height: image height
units: image units
res: image resolution
...: further arguments to plot_umap