XGR (version 1.1.7)

xEnrichRadial: Function to visualise enrichment results using radial-like plot

Description

xEnrichRadial is supposed to visualise enrichment results using radial-like plot. It returns three ggplot2 objects, the first for visualing the network with nodes lablelled by codes, the second for listing code meaning in a table, and the third for the network with nodes colored/sized with enrichment results.

Usage

xEnrichRadial(
eTerm,
ig = NULL,
fixed = T,
node.color = c("or", "adjp", "zscore"),
colormap = "grey-orange-darkred",
zlim = NULL,
node.size = c("adjp", "or", "zscore"),
slim = NULL,
node.size.range = c(0.5, 3.5),
edge.color = "skyblue",
edge.color.alpha = 0.5,
edge.curve = 0.1,
edge.arrow.gap = 0.02,
...
)

Arguments

eTerm

an object of class "eTerm" or "ls_eTerm". Alterntively, it can be a data frame having all these columns ('name','adjp','or','zscore'; 'group' optionally). Be aware that multiple ontologies are not supported here

ig

the igraph object. If provided, only those terms within it will be visualised. By default, it is NULL meaning no surch restriction

fixed

logical to indicate whether all terms in ig will be visualised. By default, it is TURE; otherwise only overlapped terms from eTerm will be visualised

node.color

which statistics will be used for node coloring. It can be "or" for the odds ratio, "adjp" for adjusted p value (FDR) and "zscore" for enrichment z-score

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

zlim

the minimum and maximum values for which colors should be plotted

node.size

which statistics will be used for node size. It can be "or" for the odds ratio, "adjp" for adjusted p value (FDR) and "zscore" for enrichment z-score

slim

the minimum and maximum values for which sizes should be plotted

node.size.range

the range of actual node size

edge.color

a character specifying which edge attribute defining the the edge colors

edge.color.alpha

the 0-1 value specifying transparency of edge colors

edge.curve

a numeric value specifying the edge curve. 0 for the straight line

edge.arrow.gap

a gap between the arrow and the node

...

additional graphic parameters used in xGGnetwork

Value

a list with 3 components, three ggplot objects (code, table, data) and an igraph object (ig appended with node attributes 'zscore', 'adjp' and 'or')

See Also

xEnrichViewer, xOBOcode, xGGnetwork

Examples

# NOT RUN {
# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"

ls_res <- xEnrichRadial(eTerm, ig, fixed=T, node.color="or",
colormap="grey-orange-darkred", zlim=c(0,7), node.size="adjp",
slim=c(0,30), node.size.range=c(1,3))
pdf("xEnrichRadial.pdf", width=6.5, height=6.5)
print(ls_res$data + coord_equal(ratio=1.3))
print(ls_res$code + coord_equal(ratio=1.3))
print(ls_res$table)
dev.off()

# advanced use: customise layout
ig.PhasedTargets <- xRDataLoader('ig.PhasedTargets',
RData.location=RData.location)
ig <- xLayout(ig.PhasedTargets,
layout="gplot.layout.fruchtermanreingold")
ls_res <- xEnrichRadial(df, ig=ig, fixed=F, node.color="or",
node.size="adjp", node.xcoord="xcoord", node.ycoord="ycoord")
pdf("xEnrichRadial.pdf", width=6.5, height=6.5)
print(ls_res$data + coord_equal())
gridExtra::grid.arrange(grobs=c(list(ls_res$code+coord_equal()),ls_res$table),
ncol=2)
dev.off()
# }