plot_dim_red: Quick way of plotting DimPlot in Seurat

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

Please run the run_dim_red function before executing this function. Internally, this function calls gg_DimPlot for 2D plotting and dim_red_3D for 3D. Please refer to these 2 functions for further parameter settings

Usage

plot_dim_red(
  input_data,
  group.by,
  DR = "pca",
  select_cells = NULL,
  dims = c(1, 2),
  return_sep = F,
  num_col = NULL,
  num_row = NULL,
  no_facet = T,
  AP = NULL,
  ...
)

Arguments

input_data	a Seurat object
group.by	a 2-element vector, parsed to the group.by argument of DimPlot in Seurat
DR	the type of dimensionality reduction method
select_cells	cells to be shown in the plot
dims	two axes of the reduced dimensional space
num_col	how many columns the subplots are arranged
no_facet	whether to use ggplot2::facet_wrap. Currently only 3D version is supported.
plot_3D	whether to plot in 3D

Value

a ggplot or list of ggplot objects

Yutong441/TBdev documentation built on Dec. 18, 2021, 8:22 p.m.