GO_viz_choose: This function provides a dot plot chart of the GO enrichments...

In neural-stem-cell-institute/screp: A Package for Enrichment Testing and Visualization of Single Cell RNA-Seq Clusters

This function provides a dot plot chart of the GO enrichments of user defined Parent term categories from the results of GO_visualizatiohn function

Description

This function provides a dot plot chart of the GO enrichments of user defined Parent term categories from the results of GO_visualizatiohn function

Usage

GO_viz_choose(
  GO_viz_results,
  chosen_cats,
  clust_list = NULL,
  markers_df = NULL,
  GOcats = NULL,
  species_x = "Homo sapiens",
  goterms = NULL
)

Arguments

GO_viz_results	object provided by the Go_visulaization function
chosen_cats	User supplied catergorical terms to plot on x-axis. Default is null which lets the function choose the categories.
clust_list	a list of gene vectors associated with each cluster.
markers_df	data frame resulting from FindAllMarkers function in the Seurat package, required if a clust_list is not provided
GOcats	product of the msigdb_gsets funciton using GOBP. Can also be user supplied annotation in the same format.
species_x	species names, default is "Homo sapiens", refer to ?msigdbr::msigdbr for available species
goterms	a vector with GOIDS as object and the GO terms as names

Value

prints a plot and returns a ggplot2 object suitable for fine tuning the appearance of the plot.

Examples

## Not run: 
GO_viz_choose(go_vis_res1,chosen_cats=newcats,markers_df=markers)

## End(Not run)

neural-stem-cell-institute/screp documentation built on Feb. 11, 2023, 10:45 a.m.