Plot spatial enrichment of contacts between two features — shaman_plot_feature

shaman_plot_feature_grid

shaman_plot_feature_grid(
  grids,
  range,
  grid_resolution,
  plot_resolution,
  type = "enrichment",
  fig_fn = "",
  fig_width = 400,
  fig_height = 400,
  pal = colorRampPalette(c("blue", "#87FFFF", "white", "#FF413D", "black")),
  zlim = c(-1, 1)
)

Arguments

grids: List of grids generated for the same two feature sets from replicate observed / expected hic tracks.
range: Window size around the grid point that was used to generate the grid.
grid_resolution: Size of bins that was used to generate the grid.
plot_resolution: Size of bins to display.
type: The type of data to plot, can be "observed" for log10(obs/sum(obs)), "expected" for log10(exp/sum(exp)) or "enrichment" for log2(obs/sum(obs) / exp/sum(exp))
fig_fn: Name of png file to output to. Empty string will cause the figure to be plotted to the current device.
fig_width: Width in pixels of output png figure.
fig_height: Height in pixels of output png figure.
pal: Color palette to use for image
zlim: The minimum and maximum values for which colors should be plotted. Suggested zlim values by type: enrichment: (-1,1), obs,exp: (-4.5, -3)

Details

After contact feature grids are generated via shaman_generate_feature_grid, use this function to visualize them.

Examples


# Set misha db to test
gsetroot(shaman_get_test_track_db())
#> Error in setwd(groot): cannot change working directory
grid <- shaman_generate_feature_grid(shaman::ctcf_forward, shaman::ctcf_reverse, "hic_obs",
    exp_track_nm = "hic_exp", score_track_nm = "hic_score"
)
#> Error in shaman_generate_feature_grid(shaman::ctcf_forward, shaman::ctcf_reverse,     "hic_obs", exp_track_nm = "hic_exp", score_track_nm = "hic_score"): Missing obs_track_nm ( hic_obs ) in track db
shaman_plot_feature_grid(list(grid), 25000, 500, 500)
#> Error: object of type 'closure' is not subsettable
shaman_plot_feature_grid(list(grid), 25000, 500, 1000)
#> Error: object of type 'closure' is not subsettable
shaman_plot_feature_grid(list(grid), 25000, 500, 2000)
#> Error: object of type 'closure' is not subsettable