XGR (version 1.1.4)

xGRmanhattan: Function to visualise genomic regions using manhattan plot

Description

xGRmanhattan is supposed to visualise genomic regions using manhattan plot. It returns an object of class "ggplot".

Usage

xGRmanhattan(gr, chromosome.only = TRUE, color = c("royalblue",
"sandybrown"), y.scale = c("normal", "sqrt", "log"), y.lab = NULL,
top = NULL, top.label.type = c("text", "box"), top.label.size = 2,
top.label.col = "black", top.label.force = 0.05, top.label.query =
NULL,
label.query.only = FALSE, top.label.chr = T, verbose = TRUE)

Arguments

gr

a GenomicRange object with a meta-column 'value'. If the meta-column 'label' is not provided, it will the name of this object

chromosome.only

logical to indicate whether only those from input data will be displayed. By default, it sets to TRUE

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)

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

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.force

the repelling force between overlapping labels

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 those in query will be displayed. By default, it sets to FALSE. It only works when labels in query are enabled/found

top.label.chr

logical to indicate whether the top hit per chromosome will be displayed. By default, it sets to TRUE. It only works when the parameter 'top' is null

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display

Value

a ggplot object.

See Also

xGRmanhattan

Examples

# NOT RUN {
# Load the library
library(XGR)
# }
# NOT RUN {
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
# }
# NOT RUN {
### GWAS catalog
GWAScatalog <- xRDataLoader('GWAScatalog',
RData.location=RData.location)
gwas <- xGR(GWAScatalog$cse_hg19, format="chr:start-end")
ind <- match(names(gwas), GWAScatalog$cse_hg19)
gwas$value <- -log10(GWAScatalog$pvalue[ind])
names(gwas) <- GWAScatalog$snp_id_current[ind]
gwas$label <- names(gwas)
gp <- xGRmanhattan(gwas)
gp
# }