Mark a gene on the pathway image

mark_gene(grob, entrez_id, fun, min_area = 0, capture = FALSE)

Arguments

grob: A grob returned by biocartaGrob().
entrez_id: A single Entrez ID.
fun: A self-defined function to add graphics to the selected gene.
min_area: Multiple polygons may be used for one single gene in the image. It can be used to select the largest polygon. The unit for calculating the area is the pixel in the image (or more properly, square pixels).
capture: It is suggested to let fun() directly return grob/gTree objects. But you can also directly use functions such as grid.points() or grid.lines() in fun((). In this case, capture must be set to TRUE to capture these graphics.

Value

If capture = FALSE, it must return a grob where new graphics are already added.

Details

fun() should be applied to each gene. It is possible an Entrez gene is mapped to multiple nodes in the image, so more precisely, fun() is applied to every node that contains the input gene.

fun() only accepts two arguments, x and y which are two vectors of xy-coordinates that define the polygon. The helper function pos_by_polygon() can be used to get positions around the polygon.

There are two ways to use fun(). First, fun() directly returns a grob. It can be a simple grob, such as by grid::pointsGrob() or complex grob by grid::gTree() and grid::gList(). Second, fun() can directly include plotting functions such as grid::grid.points(), in this case, capture argument must be set to TRUE to capture these graphics.

Examples

library(grid)
grid.newpage()
grob = biocartaGrob("h_RELAPathway")
# gene 1387 is a gene in the pathway
grob2 = mark_gene(grob, "1387", function(x, y) {
  pos = pos_by_polygon(x, y)
  pointsGrob(pos[1], pos[2], default.units = "native", pch = 16, 
    gp = gpar(col = "yellow"))
})
grid.draw(grob2)


grid.newpage()
grob3 = mark_gene(grob, "1387", function(x, y) {
  pos = pos_by_polygon(x, y)
  grid.points(pos[1], pos[2], default.units = "native", pch = 16,
    gp = gpar(col = "yellow"))
}, capture = TRUE)
grid.draw(grob3)


grid.newpage()
grob4 = mark_gene(grob, "1387", function(x, y) {
  pos = pos_by_polygon(x, y)
  pushViewport(viewport(x = pos[1] - 10, y = pos[2], 
    width = unit(4, "cm"), height = unit(4, "cm"), 
    default.units = "native", just = "right"))
  grid.rect(gp = gpar(fill = "red"))
  popViewport()
}, capture = TRUE)
grid.draw(grob4)