XGR (version 1.1.5)

xEnrichNetplot: Function to visualise enrichment results using different network layouts

Description

xEnrichNetplot is supposed to visualise enrichment results using different network layouts. Also supported is to visualise the comparative enrichment results (see the function xEnrichCompare)) with nodes/terms colored according to how many times being called significant. It returns an object of class 'igraph'.

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.

...

additional graphic parameters. See http://igraph.org/r/doc/plot.common.html for the complete list.

Value

an igraph object to represent DAG, appended with a node attribute called 'enrichment'

See Also

xEnricherGenes, xEnricherSNPs, xEnrichViewer

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/"

# 1) load eQTL mapping results: cis-eQTLs significantly induced by IFN
cis <- xRDataLoader(RData.customised='JKscience_TS2A',
RData.location=RData.location)
ind <- which(cis$IFN_t > 0 & cis$IFN_fdr < 0.05)
df_cis <- cis[ind, c('variant','Symbol','IFN_t','IFN_fdr')]
data <- df_cis$variant

# 2) Enrichment analysis using Experimental Factor Ontology (EFO)
# Considering LD SNPs and respecting ontology tree
eTerm <- xEnricherSNPs(data, ontology="EF", include.LD="EUR",
LD.r2=0.8, ontology.algorithm="lea", RData.location=RData.location)

# 3) Net plot of enrichment results
subg <- xEnrichNetplot(eTerm, top_num="auto", displayBy="fc",
node.info=c("none"), vertex.label=NA, wrap.width=30)
# }