Add Contact Map to Coverage Plot.

geom_tad2(
  matrix,
  granges,
  zlim = NULL,
  color.bias = 1,
  color.ramp = "YlOrRd",
  color.palette = NULL,
  smooth.func = NULL,
  plot.space = 0.1,
  plot.height = 1,
  top = TRUE,
  show.rect = FALSE
)

Arguments

matrix	Matrix (n x n) contains contact map information.
granges	The rownames and colnames information of matrix.
zlim	The maximum value of color to plot. Larger values will be truncated to this value.
color.bias	Bias parameter for color palette, it is the same as `bias` parameter of `colorRampPalette`. Default: 1.
color.ramp	A name of a color palette, choose from rownames of `brewer.pal.info`. Default: YlOrRd.
color.palette	A vector of colors. Overwrites the palette for `color.ramp`. Default: NULL.
smooth.func	An optional smoothing function for the matrix. Default: NULL.
plot.space	Top and bottom margin. Default: 0.1.
plot.height	The relative height of contact map to coverage plot. Default: 1.
top	Logical value, whether to place this plot on the coverage plot. Default: TRUE.
show.rect	Logical value, whether to add rect border to the plot. Default: FALSE.

Value

Plot.

Examples

library(ggcoverage)
library(HiCDataHumanIMR90)
data(Dixon2012_IMR90, package = "HiCDataHumanIMR90")
mat <- as.matrix(hic_imr90_40@.Data[[1]]@intdata)
#> 载入需要的程辑包：HiTC
#> 载入需要的程辑包：IRanges
#> 载入需要的程辑包：BiocGenerics
#> 
#> 载入程辑包：'BiocGenerics'
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#> 
#>     anyDuplicated, append, as.data.frame, basename, cbind, colnames,
#>     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
#>     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
#>     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
#>     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
#>     union, unique, unsplit, which.max, which.min
#> 载入需要的程辑包：S4Vectors
#> 载入需要的程辑包：stats4
#> 
#> 载入程辑包：'S4Vectors'
#> The following object is masked from 'package:base':
#> 
#>     expand.grid
#> 载入需要的程辑包：GenomicRanges
#> 载入需要的程辑包：GenomeInfoDb
granges <- hic_imr90_40@.Data[[1]]@xgi
# prepare coverage dataframe
df <- data.frame(
  seqnames = "chr1", start = seq(from = 50000000, to = 59999000, by = 1000),
  end = seq(from = 50001000, to = 60000000, by = 1000), score = sample(1:100, 10000, replace = TRUE),
  Type = "Example", Group = "Example"
)
# create plot
ggcoverage(
  data = df, color = "grey", region = "chr1:50000000-56000000",
  mark.region = NULL, range.position = "out"
) +
  geom_tad2(matrix = log2(mat + 1), granges = granges, zlim = 5, color.palette = c("blue", "red"))
#> Error in ggcoverage(data = df, color = "grey", region = "chr1:50000000-56000000",     mark.region = NULL, range.position = "out"): 参数没有用(region = "chr1:50000000-56000000")