Usage
xEnrichNetplot(eTerm, top_num = 10, displayBy = c("fc", "adjp", "fdr",
"zscore", "pvalue"), path.mode = c("all_paths", "shortest_paths",
"all_shortest_paths"), node.info = c("none", "term_id", "term_name",
"both",
"full_term_name"), wrap.width = 15, colormap = c("yr", "jet", "gbr",
"wyr", "br", "bwr", "rainbow", "wb"), ncolors = 40, zlim = NULL,
colorbar = T, newpage = T, glayout = layout_as_tree,
vertex.frame.color = NA, vertex.size = NULL, vertex.color = NULL,
vertex.shape = NULL, vertex.label = NULL, vertex.label.cex = NULL,
vertex.label.dist = 0.3, vertex.label.color = "blue",
edge.arrow.size = 0.3, ...)
Arguments
eTerm
an object of class "eTerm" or an object "ggplot"
(resulting from xEnrichCompare) top_num
the number of the top terms (sorted according to FDR or
adjusted p-values). If it is 'auto', only the significant terms (FDR <
0.05) will be displayed
displayBy
which statistics will be used for displaying. It can
be "fc" for enrichment fold change (by default), "adjp" or "fdr" for
adjusted p value (or FDR), "pvalue" for p value, "zscore" for
enrichment z-score
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, find all shortest paths with the equal lengths)
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, "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. By default, first 15 characters
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. "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/patttern 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
pattern is null, it always sets to false
newpage
logical to indicate whether to open a new page. By
default, it sets to true for opening a new page
glayout
either a function or a numeric matrix configuring how
the vertices will be placed on the plot. If layout is a function, this
function will be called with the graph as the single parameter to
determine the actual coordinates. This function can be one of
"layout_nicely" (previously "layout.auto"), "layout_randomly"
(previously "layout.random"), "layout_in_circle" (previously
"layout.circle"), "layout_on_sphere" (previously "layout.sphere"),
"layout_with_fr" (previously "layout.fruchterman.reingold"),
"layout_with_kk" (previously "layout.kamada.kawai"), "layout_as_tree"
(previously "layout.reingold.tilford"), "layout_with_lgl" (previously
"layout.lgl"), "layout_with_graphopt" (previously "layout.graphopt"),
"layout_with_sugiyama" (previously "layout.kamada.kawai"),
"layout_with_dh" (previously "layout.davidson.harel"),
"layout_with_drl" (previously "layout.drl"), "layout_with_gem"
(previously "layout.gem"), "layout_with_mds". A full explanation of
these layouts can be found in
http://igraph.org/r/doc/layout_nicely.html vertex.frame.color
the color of the frame of the vertices. If it
is NA, then there is no frame
vertex.size
the size of each vertex. If it is a vector, each
vertex may differ in size
vertex.color
the fill color of the vertices. If it is NA, then
there is no fill color. If the pattern is given, this setup will be
ignored
vertex.shape
the shape of each vertex. It can be one of
"circle", "square", "csquare", "rectangle", "crectangle", "vrectangle",
"pie" (http://igraph.org/r/doc/vertex.shape.pie.html), "sphere",
and "none". If it sets to NULL, these vertices with negative will be
"csquare" and the rest "circle". vertex.label
the label of the vertices. If it is NA, then there
is no label. The default vertex labels are the name attribute of the
nodes
vertex.label.cex
the font size of vertex labels.
vertex.label.dist
the distance of the label from the center of
the vertex. If it is 0 then the label is centered on the vertex. If it
is 1 then the label is displayed beside the vertex.
vertex.label.color
the color of vertex labels.
edge.arrow.size
the size of the arrows for the directed edge.
The default value is 1.