xPrioritiserManhattan: Function to visualise prioritised genes using manhattan plot

In PI: Networking Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level

Description

xPrioritiserManhattan is supposed to visualise prioritised genes using manhattan plot. Genes with the top priority are highlighed. It returns an object of class "ggplot".

Usage

xPrioritiserManhattan(pNode, color = c("darkred", "darkgreen"), cex =
0.5,
highlight.top = 20, highlight.col = "deepskyblue",
highlight.label.size = 2, highlight.label.offset = 0.02,
highlight.label.col = "darkblue", verbose = T,
RData.location =
"https://github.com/hfang-bristol/RDataCentre/blob/master/XGR/1.0.0")

Arguments

pNode	an object of class "pNode"
color	a character vector for point colors to alternate
cex	a numeric value for point size
highlight.top	the number of the top targets to be highlighted
highlight.col	the highlight colors
highlight.label.size	the highlight label size
highlight.label.offset	the highlight label offset
highlight.label.col	the highlight label color
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display
RData.location	the characters to tell the location of built-in RData files. See xRDataLoader for details

Value

an object of class "ggplot"

Note

none

See Also

xRDataLoader, xPrioritiser, xPrioritiserSNPs, xPrioritiserGenes, xPrioritiserPathways

Examples

## Not run: 
# Load the library
library(XGR)
library(igraph)
library(dnet)
library(ggbio)

# a) provide the SNPs with the significance info
## get lead SNPs reported in AS GWAS and their significance info (p-values)
AS <- read.delim(file.path(path.package("XGR"),"AS.txt"),
stringsAsFactors=FALSE)

# b) perform priority analysis
pNode <- xPrioritiserSNPs(data=AS,
network="PCommonsUN_medium",restart=0.7)

# c) manhattan plot
mp <- xPrioritiserManhattan(pNode, highlight.top=10)
#pdf(file="Gene_manhattan.pdf", height=6, width=12, compress=TRUE)
print(mp)
#dev.off()

## End(Not run)

PI documentation built on May 2, 2019, 5:25 p.m.