get_all_path_view: Pathview
In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description Usage Arguments

Plot the average expression of a list of genes in one cell type on pathview plots for the major pathways in embryological development.

get_all_path_view(
  genes,
  markers,
  cell_type,
  organism_db,
  save_dir,
  pathway_db = NULL,
  cluster_col = "feature",
  organism_name = "human",
  ...
)

`markers`	a dataframe of gene expression. It can be generated from `find_DE_genes`
`cell_type`	which cell type to analyse
`organism_db`	the database for the organism to be investigated
`save_dir`	where to save the results
`pathway_db`	a dataframe with 2 columns: 'pathway' for the common names of the pathway that is used for naming the output file, and 'kegg_id' for the KEGG ID for that pathway. This ID may be obtained from: https://www.genome.jp/kegg/pathway.html
`gene`	a vector of gene names