plot_cells: Plot cells of a monocle cell data set

In whtns/seuratTools: Tools for Managing Seurat Objects

Plot cells of a monocle cell data set

Description

Plot cells of a monocle cell data set

Usage

plot_cells(
  cds,
  x = 1,
  y = 2,
  reduction_method = c("UMAP", "tSNE", "PCA", "LSI", "Aligned"),
  color_cells_by = "cluster",
  group_cells_by = c("cluster", "partition"),
  genes = NULL,
  show_trajectory_graph = TRUE,
  trajectory_graph_color = "grey28",
  trajectory_graph_segment_size = 0.75,
  norm_method = c("log", "size_only"),
  label_cell_groups = TRUE,
  label_groups_by_cluster = TRUE,
  group_label_size = 2,
  labels_per_group = 1,
  label_branch_points = TRUE,
  label_roots = TRUE,
  label_leaves = TRUE,
  graph_label_size = 2,
  cell_size = 0.35,
  cell_stroke = I(cell_size/2),
  alpha = 1,
  min_expr = 0.1,
  rasterize = FALSE,
  scale_to_range = FALSE,
  ...
)

Arguments

...

whtns/seuratTools documentation built on Oct. 28, 2024, 7:18 a.m.