shaman_plot_feature_grid: Plot spatial enrichment of contacts between two features

In tanaylab/shaman: shaman - Sampling HiC contAct Matrices for Aparametric Normalization

Plot spatial enrichment of contacts between two features

Description

shaman_plot_feature_grid

Usage

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())
grid <- shaman_generate_feature_grid(shaman::ctcf_forward, shaman::ctcf_reverse, "hic_obs",
    exp_track_nm = "hic_exp", score_track_nm = "hic_score"
)
shaman_plot_feature_grid(list(grid), 25000, 500, 500)
shaman_plot_feature_grid(list(grid), 25000, 500, 1000)
shaman_plot_feature_grid(list(grid), 25000, 500, 2000)

tanaylab/shaman documentation built on April 2, 2022, 1:32 a.m.