xPierManhattan: Function to visualise prioritised genes using manhattan plot

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

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"),
point.size = 0.5,
top = 50,
top.label.type = c("box", "text"),
top.label.size = 2,
top.label.col = "darkblue",
top.label.query = NULL,
label.query.only = FALSE,
chromosome.only = TRUE,
y.scale = c("normal", "sqrt", "log"),
y.lab = NULL,
GR.Gene = c("UCSC_knownGene", "UCSC_knownCanonical"),
font.family = "sans",
signature = TRUE,
verbose = TRUE,
RData.location = "http://galahad.well.ox.ac.uk/bigdata",
guid = NULL,
...
)

Arguments

pNode	an object of class "pNode" (or "sTarget" or "dTarget")
color	a character vector for colors to alternate chromosome colorings. If NULL, ggplot2 default colors will be used. If a single character is provided, it can be "jet" (jet colormap) or "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta)
point.size	the point size
top	the number of the top targets to be labelled/highlighted
top.label.type	how to label the top targets. It can be "box" drawing a box around the labels , and "text" for the text only
top.label.size	the highlight label size
top.label.col	the highlight label color
top.label.query	which top genes in query will be labelled. By default, it sets to NULL meaning all top genes will be displayed. If labels in query can not be found, then all will be displayed
label.query.only	logical to indicate whether only genes in query will be displayed. By default, it sets to FALSE. It only works when labels in query are enabled/found
chromosome.only	logical to indicate whether only genes from input data will be displayed. By default, it sets to TRUE
y.scale	how to transform the y scale. It can be "normal" for no transformation, "sqrt" for square root transformation, and "log" for log-based transformation
y.lab	the y labelling. If NULL (by default), it shows the column of input data
GR.Gene	the genomic regions of genes. By default, it is 'UCSC_knownGene', that is, UCSC known genes (together with genomic locations) based on human genome assembly hg19. It can be 'UCSC_knownCanonical', that is, UCSC known canonical genes (together with genomic locations) based on human genome assembly hg19. Alternatively, 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"
font.family	the font family for texts
signature	logical to indicate whether the signature is assigned to the plot caption. By default, it sets TRUE
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
guid	a valid (5-character) Global Unique IDentifier for an OSF project. See xRDataLoader for details
...	additional paramters associated with ggrepel::geom_text_repel

Value

an object of class "ggplot", appended by an GR object called 'gr'

Note

none

See Also

xRDataLoader, xColormap

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
# 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)
ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase',
RData.location=RData.location)
gr <- ImmunoBase$AS$variants
AS <- as.data.frame(GenomicRanges::mcols(gr)[, c('Variant','Pvalue')])

# b) perform priority analysis
pNode <- xPierSNPs(data=AS, include.eQTL="JKng_mono",
include.HiC='Monocytes', network="PCommonsUN_medium", restart=0.7,
RData.location=RData.location)

# c) manhattan plot
## default plot
mp <- xPierManhattan(pNode, RData.location=RData.location)
#pdf(file="Gene_manhattan.pdf", height=6, width=12, compress=TRUE)
print(mp)
#dev.off()
mp$gr
## control visuals
mp <- xPierManhattan(pNode, color='ggplot2', top=50,
top.label.col="black", y.scale="sqrt", RData.location=RData.location)
mp
## control labels
# only IL genes will be labelled
ind <- grep('^IL', rownames(pNode$priority))
top.label.query <- rownames(pNode$priority)[ind]
mp <- xPierManhattan(pNode, top.label.query=top.label.query,
RData.location=RData.location)
mp
# only IL genes will be displayed
mp <- xPierManhattan(pNode, top.label.query=top.label.query,
label.query.only=TRUE, RData.location=RData.location)
mp

## End(Not run)

Pi documentation built on Nov. 29, 2021, 3 p.m.