DAreport: Create visualization HTML

In martahidalgo/hipathia: HiPathia: High-throughput Pathway Analysis

Create visualization HTML

Description

Saves the results of a DAdata comparison for the Hipathia pathway values into a folder, and creates a HTML from which to visualize the results on top of the pathways. The results are stored into the specified folder. If this folder does not exist, it will be created. The parent folder must exist.

Usage

DAreport(
  DAdata,
  pathways,
  conf.level = 0.05,
  adjust = TRUE,
  group_by = "pathway",
  colors = "classic",
  output_folder = NULL,
  path = NULL,
  verbose = TRUE
)

Arguments

DAdata	List of comparison results, returned by function DAcomp.
pathways	Pathways object as returned by the load_pathways function
conf.level	Level of significance. By default 0.05.
adjust	Boolean, whether to adjust the p.value with Benjamini-Hochberg FDR method. Default is TRUE.
group_by	How to group the subpathways to be visualized. By default they are grouped by the pathway to which they belong. Available groupings include "uniprot", to group subpathways by their annotated Uniprot functions, "GO", to group subpathways by their annotated GO terms, and "genes", to group subpathways by the genes they include. Default is set to "pathway".
colors	String with the color scheme or vector of colors to be used. See define_colors for available options. Default is "hiro".
output_folder	Name of the folder in which the report will be stored.
path	Absolute path to the parent directory in which 'output_folder' will be saved. If it is not provided, it will be created in a temp folder.
verbose	Boolean, whether to show details about the results of the execution

Value

Saves the results and creates a report to visualize them through a server in the specified output_folder. Returns the folder where the report has been stored.

Examples

data(DAdata)
pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
"hsa04012"))
DAreport(DAdata, pathways)

martahidalgo/hipathia documentation built on Jan. 12, 2023, 1:44 p.m.