xGRkaryogram | R Documentation |
xGRkaryogram
is supposed to visualise genomic regions using
manhattan plot. It returns an object of class "ggplot".
xGRkaryogram(gr, cytoband = F, color = "royalblue", size = 0.5, label = F, label.size = 2, label.col = "magenta", label.force = 0.05, label.query = NULL, verbose = T, RData.location = "http://galahad.well.ox.ac.uk/bigdata")
gr |
a GenomicRange object. If the meta-column 'label' is not provided, it will the name of this object |
cytoband |
logical to indicate whether cytoband will be displayed. By default, it sets to false |
color |
the rect color. By default it is 'royalblue' |
size |
the rect size |
label |
logical to indicate whether to label the rect. By default, it sets to false |
label.size |
the label size |
label.col |
the label color ('magenta' by default) |
label.force |
the repelling force between overlapping labels |
label.query |
only query will be labelled. By default, it sets to NULL meaning all will be displayed. If labels in query can not be found, then all will be displayed |
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 |
a ggplot object.
none
xGRkaryogram
## 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) names(gwas) <- GWAScatalog$snp_id_current[ind] gwas$label <- names(gwas) gp <- xGRkaryogram(gwas) gp ## End(Not run)