R: Function to visualise prioritised genes using manhattan plot

xPierManhattan

R Documentation

Function to visualise prioritised genes using manhattan plot

Description

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

Usage

xPierManhattan(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", GR.Gene = "UCSC_genes", verbose = T,
RData.location =
"https://github.com/hfang-bristol/RDataCentre/blob/master/Portal")

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
`GR.Gene`	the genomic regions of genes. By default, it is 'UCSC_genes', that is, UCSC known canonical genes (together with genomic locations) based on human genome assembly hg19. Even the user can specify the customised input. To do so, first save your RData file (containing an GR object) into your local computer, and make sure the GR object content names refer to Gene Symbols. Then, tell "GR.Gene" with your RData file name (with or without extension), plus specify your file RData path in "RData.location"
`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

Examples

## Not run: 
# Load the library
library(Pi)

# a) provide the SNPs with the significance info
## get lead SNPs reported in AS GWAS and their significance info (p-values)
data.file <- "http://galahad.well.ox.ac.uk/bigdata/AS.txt"
AS <- read.delim(data.file, header=TRUE, stringsAsFactors=FALSE)

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

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

## End(Not run)