Add Links to Coverage Plot.

geom_link(
  link.file,
  file.type = "bedpe",
  score.col = NULL,
  score.threshold = NULL,
  score.color = c("blue", "grey", "red"),
  scale.range = 10,
  plot.space = 0.1,
  plot.height = 0.2,
  show.rect = FALSE
)

Arguments

link.file	File contains region link information.
file.type	The type of `link.file`, choose from bedpe, pairs. Default: bedpe.
score.col	Column index contains score information, used when `file.type` is bedpe. Default: NULL.
score.threshold	The score threshold, used when `score.col` is not NULL. Default: NULL.
score.color	The score color vector. The length should be three, the first represents the lowest score, the second represents the middle score, the third represents the highest score. Default: c("blue", "grey", "red").
scale.range	Scale the height of link according to width, should be greater than or equal to 1 (not scale). Default: 10.
plot.space	Top and bottom margin. Default: 0.1.
plot.height	The relative height of link to coverage plot. Default: 0.2.
show.rect	Logical value, whether to add rect border to the plot. Default: FALSE.

Value

Plot.

References

https://stuartlab.org/signac/articles/cicero.html

Examples

library(ggcoverage)
# create test dataframe (random)
df <- data.frame(
  seqnames = "chr9", start = seq(from = 4000000, to = 5999000, by = 1000),
  end = seq(from = 4001000, to = 6000000, by = 1000), score = sample(1:100, 2000, replace = TRUE),
  Type = "Example", Group = "Example"
)
# create plot
ggcoverage(
  data = df, color = "grey", region = "chr9:4000000-6000000",
  mark.region = NULL, range.position = "out"
) +
  geom_link(link.file = link.file, file.type = "bedpe", show.rect = TRUE)
#> Error in ggcoverage(data = df, color = "grey", region = "chr9:4000000-6000000",     mark.region = NULL, range.position = "out"): 参数没有用(region = "chr9:4000000-6000000")