Usage
visEnrichment(e, nodes_query = NULL, path.mode =
c("all_shortest_paths",
"shortest_paths", "all_paths"), data.type = c("adjp", "pvalue",
"zscore"),
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("left_right", "top_bottom",
"bottom_top", "right_left"), node.info = c("both", "none", "term_id",
"term_name", "full_term_name"), graph.node.attrs = NULL,
graph.edge.attrs = NULL, node.attrs = NULL)Arguments
nodes_query
a verctor containing a list of
nodes/terms in query. These nodes are used to produce a
subgraph of the ontology DAG induced by them. If NULL,
the top 5 significant terms (in terms of adjusted
p-value) will be used
path.mode
the mode of paths induced by nodes in
query. 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, fi
data.type
a character telling which data type for
nodes in query is used to color-code nodes. It can be one
of 'adjp' for adjusted p-values (by default), 'pvalue'
for p-values and 'zscore' for z-scores. When 'adjp' or
'pvalue' is used, 10-based negative logarithm i
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 "yr" (yellow-red colormap; by default), "jet" (jet
colormap), "bwr" (blue-white-red colormap), "gbr"
(green-black-red colormap), "wyr" (white-yellow-red
colormap), "br" (black-red colormap), "wb" (white-black
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; by default),
"top_bottom" for the top-bottom layout, "bottom_top" for
the bottom-top layout, and "right_left" for the
right-left la
node.info
tells the ontology term information used
to label nodes. It can be one of "both" for using both of
Term ID and Name (the first 15 characters; by default),
"none" for no node labeling, "term_id" for using Term ID,
"term_name" for using Term Name (the first
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