Select branching paths from a 'Cell Dataset' object from Monocle3

Source: R/m3_select_path.R

`m3_select_path()` helps select branching paths from a from a 'Cell Dataset' object from Monocle3 TI Analysis. This function also has an in-built shiny app thats enabled interactive selection.

m3_select_path(
  cds,
  latent_space = "umap",
  anno_col = "cell_type",
  ptime_col = "Pseudotime",
  path_col = "Path",
  use_shiny = TRUE,
  plot_purity = FALSE,
  m3_pp = list(root_pp = c(""), path1_pp = c(""), path2_pp = c(""), path1_name = NULL,
    path2_name = NULL)
)

Arguments

cds

An object from Monocle3.

latent_space

Latent dimension to use for the plotting. (Default is "umap")

anno_col

A character string representing the column name for cell level metadata containing cell level annotations. (Default is "cell_type").

ptime_col

A character string representing the column name for inferred Pseudotime values. (Default is "Pseudotime")

path_col

A character string representing the column name for branching path assignment. (Default is `path_prefix`)

use_shiny

Enable the selection for shiny-selection wizard. (Default is TRUE)

plot_purity

Plot a bar plot, showing the the principal points against the of `anno_col`. This will show the count of annotations for each of the principal points. (Default is TRUE)

m3_pp

A list containing the character vectors for principal points ("Y_") to be used for the branch selection. See examples.

Value

An object of class ScMaSigPro, subsetted based on the specified paths.

Author

Priyansh Srivastava spriyansh29@gmail.com