xA2IO: Function to construct an immune ontology

In A2: Atlas and Analysis of Systems-Biology-Led Pathways

Description

xA2IO is supposed to construct an immune ontology.

Usage

xA2IO(cutoff.anno = 15, colormap = "ggplot2", filename = "xA2IO",
verbose = TRUE, RData.location =
"http://galahad.well.ox.ac.uk/bigdata")

Arguments

cutoff.anno	an integer specifying the annotation cutoff obove which ontology terms are considered
colormap	short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta), and "ggplot2" (emulating ggplot2 default color palette). Alternatively, any hyphen-separated HTML color names, e.g. "lightyellow-orange" (by default), "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names
filename	the without-extension part of the name of the output file. By default, it is 'xA2GraphML'
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display
RData.location	the characters to tell the location of built-in RData files. See xRDataLoader for details

Value

a list with 3 components, two ggplot objects (code and table) and an igraph object (ig) having attributes:

• name: a node attribute for name (ie node.code)

• term_id: a node attribute for term_id (the primary source)

• term_name: a node attribute for term_name (the primary source)

• term_distance: a node attribute for term_distance (starting with 0, 1, ...)

• term_namespace: a node attribute for term_namespace (ie IO, Disease, Function, Phenotype)

• anno: a node attribute as a list storing annotated gene symbols

• net: a node attribute as a list storing connectivity between genes

• path: a node attribute as a list storing pathways enriched

• node.label: a node attribute for the node label in the form of '[nAnno->nNode@nEdge->nPath] term_name'

• node.label.size: a node attribute for the node label size (decreasing radiately)

• node.label.color: a node attribute for the node label color (grouped by the subontologies)

• xcoord: a node attribute for the node x coordinate

• ycoord: a node attribute for the node y coordinate

• node.code: a node attribute for the 3-letter node code, 1st letter for the subontology, 2nd for the distance, 3rd for the sequential order at the same distance

• node.table: a node attribute for the node label in the lookup table

• edge.color: an edge attribute for the edge color (grouped by the subontologies)

Note

none

See Also

xA2IO

Examples

# Load the library
library(A2)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev/"

## Not run: 
ls_IO <- xA2IO(RData.location=RData.location)
ls_IO$ig
ls_IO$code
ls_IO$table

lapply(V(ls_IO$ig)[['b5c']]$path, function(x) xA2GraphML(query=x,
filename=x, RData.location=RData.location))

## End(Not run)

A2 documentation built on May 2, 2019, 5 p.m.