reactome_visualization: reactome_visualization

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

reactome_visualization

Description

function to generate plot using the dataframe from the reactome_prep function

Usage

reactome_visualization(RP.df, RP_adj, RP = NULL, path_order = NULL)

Arguments

RP.df	data frame produced by reactome_prep function
RP_adj	same data frame as used in reactome_prep function
RP	data frame of Path IDS from Reactome database. IF left null uses the RP file included as data in the screp package.
path_order	a vector of parent pathway names from the rootName column in the RP.df. Can be used to plot the parent pathway names in desired order along the x-axis. Default is NULL which gives a random order.

Value

returns a list with the first item in the list being a data frame used in creating a plotting object and the second item being the ggplot2 object generated

Examples

## Not run: 
react_vis2<-reactome_visualization(RP_ready,mRPR,path_order=z)

## End(Not run)

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