XGR (version 1.1.5)

xEnrichDAGplotAdv: Function to visualise comparative enrichment results using a direct acyclic graph (DAG)

Description

xEnrichDAGplotAdv is supposed to visualise the comparative enrichment results (see the function xEnrichCompare)) using a direct acyclic graph (DAG). Nodes/terms can be colored according to how many times being called significant. If two enrichment results are compared, node names are prefixed with the form of 'x1-x2', where x1 is for result 1 and x2 for result 2 (the value for x1 or x2 can be '0' for being insignificant, and '1' for being significant). It takes input an 'ggplot' object (with two componets alreadly appended 'g' and 'data'), and returns an object of class 'Ragraph'.

Usage

xEnrichDAGplotAdv(ggplot, displayBy = c("nSig", "none"),
path.mode = c("all_paths", "shortest_paths", "all_shortest_paths"),
height = 7, width = 7, margin = rep(0.1, 4),
colormap = c("white-lightcyan-cyan", "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("term_name", "term_id", "none"),
wrap.width = NULL, graph.node.attrs = NULL,
graph.edge.attrs = NULL, node.attrs = NULL)

Arguments

ggplot

an object "ggplot" (resulting from xEnrichCompare)

displayBy

which statistics will be used for displaying. It can be "nSig" for how many times being called significant (by default), "none" for no color-coding on nodes/terms

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)

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 "term_id" for using Term ID, "term_name" for using Term Name, 'none' for no labellings

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

Value

An object of class 'Ragraph'

See Also

xEnrichCompare

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)
# 2a) Without considering LD SNPs and without respecting ontology tree
eTerm_noLD_noTree <- xEnricherSNPs(data, ontology="EF_disease",
include.LD=NA, ontology.algorithm="none",
RData.location=RData.location)
# 2b) Without considering LD SNPs but respecting ontology tree
eTerm_noLD_Tree <- xEnricherSNPs(data, ontology="EF_disease",
include.LD=NA, ontology.algorithm="lea", RData.location=RData.location)
# 2c) Considering LD SNPs but without respecting ontology tree
eTerm_LD_noTree <- xEnricherSNPs(data, ontology="EF_disease",
include.LD="EUR", LD.r2=0.8, ontology.algorithm="none",
RData.location=RData.location)
# 2d) Considering LD SNPs and respecting ontology tree
eTerm_LD_Tree <- xEnricherSNPs(data, ontology="EF_disease",
include.LD="EUR", LD.r2=0.8, ontology.algorithm="lea",
RData.location=RData.location)

# 3) Compare enrichment results
list_eTerm <- list(eTerm_noLD_noTree, eTerm_noLD_Tree, eTerm_LD_noTree,
eTerm_LD_Tree)
names(list_eTerm) <- c('LD (-) & Tree (-)', 'LD (-) & Tree (+)', 'LD
(+) & Tree (-)', 'LD (+) & Tree (+)')
## side-by-side comparisons 
bp <- xEnrichCompare(list_eTerm, displayBy="fc")
#pdf(file="enrichment_compared.pdf", height=6, width=12, compress=TRUE)
print(bp)
#dev.off()

# 4) DAGplot of comparative enrichment results in the context of ontology tree
xEnrichDAGplotAdv(bp, graph.node.attrs=list(fontsize=100))
# }