Draw a BioCarta pathway

grid.biocarta(
  pathway,
  color = NULL,
  x = unit(0.5, "npc"),
  y = unit(0.5, "npc"),
  width = NULL,
  height = NULL,
  just = "centre",
  default.units = "npc",
  name = NULL
)

biocartaGrob(
  pathway,
  color = NULL,
  x = unit(0.5, "npc"),
  y = unit(0.5, "npc"),
  width = NULL,
  height = NULL,
  just = "centre",
  default.units = "npc",
  name = NULL
)

Arguments

pathway: A BioCarta pathway ID, a MSigDB ID or a biocarta_pathway object. All valid BioCarta pathway IDs are in all_pathways(). The list of MSigDB IDs for BioCarta pathways can be found at https://www.gsea-msigdb.org/gsea/msigdb/human/genesets.jsp?collection=CP:BIOCARTA.
color: A named vector where names should correspond to Entrez IDs.
x: A numeric vector or unit object specifying x-location.
y: A numeric vector or unit object specifying y-location.
width: A numeric vector or unit object specifying width.
height: A numeric vector or unit object specifying width.
just: The same as in grid::viewport().
default.units: The same as in grid::viewport().
name: The same as in grid::viewport().

Value

biocartaGrob() returns a gTree object.

Details

The graphics object contains a pathway image and genes highlighted on the image.

The aspect ratio of the image is kept. If one of width and height is set, the other dimension is calculated by the aspect ratio. If both of width and height is set or inherit from parent viewport, the width and height are automatically adjust to let one dimension completely fill the viewport.

Examples

library(grid)
grid.newpage()
grid.biocarta("h_RELAPathway")


grob = biocartaGrob("h_RELAPathway")