xEnrichDAGplotAdv: Function to visualise comparative enrichment results using a...

In hfang-bristol/XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

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'

Note

A list of global node attributes used in "graph.node.attrs":

• "shape": the shape of the node: "circle", "rectangle", "rect", "box" and "ellipse"

• "fixedsize": the logical to use only width and height attributes. By default, it sets to true for not expanding for the width of the label

• "fillcolor": the background color of the node

• "color": the color for the node, corresponding to the outside edge of the node

• "fontcolor": the color for the node text/labelings

• "fontsize": the font size for the node text/labelings

• "height": the height (in inches) of the node: 0.5 by default

• "width": the width (in inches) of the node: 0.75 by default

• "style": the line style for the node: "solid", "dashed", "dotted", "invis" and "bold"

A list of global edge attributes used in "graph.edge.attrs":

• "color": the color of the edge: gray by default

• "weight": the weight of the edge: 1 by default

• "style": the line style for the edge: "solid", "dashed", "dotted", "invis" and "bold"

A list of local node attributes used in "node.attrs" (only those named Term IDs will be changed locally!):

• "label": a named vector specifying the node text/labelings

• "shape": a named vector specifying the shape of the node: "circle", "rectangle", "rect", "box" and "ellipse"

• "fixedsize": a named vector specifying whether it sets to true for not expanding for the width of the label

• "fillcolor": a named vector specifying the background color of the node

• "color": a named vector specifying the color for the node, corresponding to the outside edge of the node

• "fontcolor": a named vector specifying the color for the node text/labelings

• "fontsize": a named vector specifying the font size for the node text/labelings

• "height": a named vector specifying the height (in inches) of the node: 0.5 by default

• "width": a named vector specifying the width (in inches) of the node: 0.75 by default

• "style": a named vector specifying the line style for the node: "solid", "dashed", "dotted", "invis" and "bold"

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))

## End(Not run)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.