plot a normlized hic map

Source: R/shaman_plot_map.R

shaman_golot_map_score

shaman_gplot_map_score(
  points_score,
  interval_range = NA,
  rotate = TRUE,
  point_size = 0.1,
  add_axis = TRUE
)

Arguments

points_score

A dataframe containing the points (start1, start2) and their normalized score.

rotate

Binary flag, indicating if the plot should be rotated by 45 degrees.

point_size

Cex size of the points in the plot.

add_axis

Binary flag, indicating if axis should be added to plot.

Value

gplot containing the map

Details

Plots observerved hic contact matrix color-coded by normalized scores. Data can be either extracted directly from score track or computed via the functions: score_hic_mat, shuffle_and_score_hic_mat

Examples


# Set misha db to test
gsetroot(shaman_get_test_track_db())
#> Error in setwd(groot): cannot change working directory
points <- gextract("hic_score", gintervals.2d(2, 175e06, 178e06, 2, 175e06, 178e06), colnames = "score")
#> Error: Invalid interval (chr2, 1.75e+08, 1.78e+08): end coordinate exceeds chromosome boundaries
shaman_gplot_map_score(points)
#> Error in shaman_gplot_map_score(points): points_score data frame must contain the following columns: start1, start2, score