xPrioritiserManhattan: Function to visualise prioritised genes using manhattan plot

Description Usage Arguments Value Note See Also Examples

View source: R/xPrioritiserManhattan.r

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

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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

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## 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 31, 2017, 3:30 a.m.

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