xGRmanhattan | R Documentation

## 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.

### Note

none

### See Also

`xGRmanhattan`

### Examples

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

    ## End(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

    ## End(Not run)