dnet (version 1.0.0)

visDAG: Function to visualise a direct acyclic graph (DAG) with node colorings according to a named input data vector (if provided)

Description

visDAG is supposed to visualise a direct acyclic graph (DAG) with node colorings according to a named input data vector (if provided)

Usage

visDAG(g, data = NULL, height = 7, width = 7, margin = rep(0.1, 4),
colormap = c("lightyellow-orange", "yr", "bwr", "jet", "gbr", "wyr",
"br",
"rainbow", "wb"), ncolors = 40, zlim = NULL, colorbar = T,
colorbar.fraction = 0.1, newpage = T,
layout.orientation = c("left_right", "top_bottom", "bottom_top",
"right_left"), node.info = c("none", "term_id", "term_name", "both",
"full_term_name"), graph.node.attrs = NULL, graph.edge.attrs = NULL,
node.attrs = NULL)

Arguments

g

an object of class "igraph"

data

a named input data verctor used to color-code vertices/nodes. The input data vector must have names, and these names should include all node names of input graph, i.e. V(g)$name, since there is a mapping operation. The way of how to color-code is to map v

height

a numeric value specifying the height of device

width

a numeric value specifying the width of device

margin

margins as units of length 4 or 1

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), a

ncolors

the number of colors specified over the colormap

zlim

the minimum and maximum z/data values for which colors should be plotted, defaulting to the range of the finite values of z. Each of the given colors will be used to color an equispaced interval of this range. The midpoints of the intervals cover the rang

colorbar

logical to indicate whether to append a colorbar. If data is null, it always sets to false

colorbar.fraction

the relative fraction of colorbar block against the device size

newpage

logical to indicate whether to open a new page. By default, it sets to true for opening a new page

layout.orientation

the orientation of the DAG layout. It can be one of "left_right" for the left-right layout (viewed from the DAG root point), "top_bottom" for the top-bottom layout, "bottom_top" for the bottom-top layout, and "right_left" for the right-left layout

node.info

tells the ontology term information used to label nodes. It can be one of "none" for no node labeling, "term_id" for using Term ID, "term_name" for using Term Name (the first 15 characters), "both" for using both of Term ID and Name (the first 15 characte

graph.node.attrs

a list of global node attributes. These node attributes will be changed globally. See 'Note' below for details on the attributes

graph.edge.attrs

a list of global edge attributes. These edge attributes will be changed globally. See 'Note' below for details on the attributes

node.attrs

a list of local edge attributes. These node attributes will be changed locally; as such, for each attribute, the input value must be a named vector (i.e. using Term ID as names). See 'Note' below for details on the attributes

Value

• An object of class 'Ragraph'

itemize

• "label": a named vector specifying the node text/labelings

item

• "weight": the weight of the edge: 1 by default
• "style": the line style for the edge: "solid", "dashed", "dotted", "invis" and "bold"
• "shape": a named vector specifying the shape of the node: "circle", "rectangle", "rect", "box" and "ellipse"
• "fixedsize": a named vector specifying whether it sets to true for not expanding for the width of the label
• "fillcolor": a named vector specifying the background color of the node
• "color": a named vector specifying the color for the node, corresponding to the outside edge of the node
• "fontcolor": a named vector specifying the color for the node text/labelings
• "fontsize": a named vector specifying the font size for the node text/labelings
• "height": a named vector specifying the height (in inches) of the node: 0.5 by default
• "width": a named vector specifying the width (in inches) of the node: 0.75 by default
• "style": a named vector specifying the line style for the node: "solid", "dashed", "dotted", "invis" and "bold"

See Also

dDAGreverse, dDAGroot, dDAGinduce, dDAGlevel

Examples

# 1) load GO Molelular Function as igraph object
load(url("http://dnet.r-forge.r-project.org/data/Obo/ig.GOMF.RData"))
g <- ig.GOMF

# 2) randomly select vertices as the query nodes
# the more common, the query nodes can be term id
nodes_query <- V(g)[sample(V(g),5)]$name

# 3) obtain the induced subgraph based on all possible paths
subg <- dDAGinduce(g, nodes_query, path.mode="all_paths")

# 4) just visualise the induced subgraph
visDAG(g=subg, node.info="both")

# 5) color-code nodes/terms according to its level
data <- dDAGlevel(subg)
visDAG(g=subg, data=data, node.info="both")
# 5a) globally change the node and edge attributes
visDAG(g=subg, data=data, layout.orientation="top_bottom",
node.info="both",
graph.node.attrs=list(fixedsize=FALSE,shape="box",color="transparent"),
graph.edge.attrs=list(color="black"))
# 5b) locally highlight the root by changing its shape into "box"
root <- dDAGroot(subg)
root.shape <- "box"
names(root.shape) <- V(subg)[root]$name
visDAG(g=subg, data=data, node.info="both",
node.attrs=list(shape=root.shape))
# 5c) further locally remove the root labelling
root.label <- ""
names(root.label) <- V(subg)[root]$name
visDAG(g=subg, data=data, node.info="both",
node.attrs=list(shape=root.shape,label=root.label))