Usage
xSocialiserDAGplot(g, query, displayBy = c("IC", "none"),
path.mode = c("all_paths", "shortest_paths", "all_shortest_paths"),
height = 7, width = 7, margin = rep(0.1, 4), colormap = c("yr", "bwr",
"jet", "gbr", "wyr", "br", "rainbow", "wb", "lightyellow-orange"),
ncolors = 40, zlim = NULL, colorbar = T, colorbar.fraction = 0.1,
newpage = T, layout.orientation = c("top_bottom", "left_right",
"bottom_top", "right_left"), node.info = c("none", "term_id",
"term_name",
"both", "full_term_name"), wrap.width = NULL, graph.node.attrs = NULL,
graph.edge.attrs = NULL, node.attrs = NULL, output.format =
c("Ragraph",
"igraph"))
Arguments
g
an object of class "igraph" (resulting from similarity
analysis)
query
an object in query (for example, an SNP or Gene)
displayBy
which statistics will be used for displaying. It can
be "IC" for information content (by default), "none" for no
color-coding on nodes/terms
path.mode
the mode of paths induced by nodes/terms. It can be
"all_paths" for all possible paths to the root, "shortest_paths" for
only one path to the root (for each node in query),
"all_shortest_paths" for all shortest paths to the root (i.e. for each
node, find all shortest paths with the equal lengths)
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), and
"rainbow" (rainbow colormap, that is,
red-yellow-green-cyan-blue-magenta). 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 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 range, so that
values just outside the range will be plotted
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
characters), and "full_term_name" for using the full Term Name
wrap.width
a positive integer specifying wrap width of Term
Name
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
output.format
the format specifying the return value. It can be
"Ragraph" (by default) or "igraph"