Automatically generate alter_fun
Automatically generate alter_fun
alter_graphic(graphic = c("rect", "point"),
width = 1, height = 1,
horiz_margin = unit(1, "pt"), vertical_margin = unit(1, "pt"),
fill = "red", col = NA, pch = 16, ...)graphic |
Graphic to draw. |
width |
Relative width of the rectangle. |
height |
Relative height of the rectangle. |
horiz_margin |
Horizontal margin. E.g. if you want 1mm margin on top and 1mm margin at bottom of the rectangle, set this value to |
vertical_margin |
Vertical margin. |
fill |
Filled color. |
col |
Border color. |
pch |
Pch for points |
... |
Pass to |
This function aims to simplify the definition of functions in alter_fun. Now it only
supports rectangles and points.
mat = read.table(textConnection(
"s1,s2,s3
g1,snv;indel,snv,indel
g2,,snv;indel,snv
g3,snv,,indel;snv"), row.names = 1, header = TRUE, sep = ",", stringsAsFactors = FALSE)
mat = as.matrix(mat)
col = c(snv = "red", indel = "blue")
oncoPrint(mat,
alter_fun = list(
snv = alter_graphic("rect", width = 0.9, height = 0.9, fill = col["snv"]),
indel = alter_graphic("rect", width = 0.9, height = 0.9, fill = col["indel"])
), col = col)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.