tornado_insulation: Plot a heatmap or profile of insulation scores
In robinweide/GENOVA: GENOVA: expore the Hi-C

tornado_insulation

R Documentation

Plot a heatmap or profile of insulation scores

Description

Takes pre-calculated insulation scores around a set of genomic locations and plots these in a heatmap and/or profile.

Usage

tornado_insulation(
  IS_discovery,
  bed,
  bed_pos = "end",
  region_width = 1e+06,
  sort_bins = 11,
  sort_on = 1,
  mode = c("both", "heatmap", "profile"),
  colour_lim = c(-1, 1),
  colours = NULL,
  profile_fun = mean,
  custom_fill_scale = NULL,
  profile_ylim = NULL,
  title = NULL
)

Arguments

`IS_discovery`	A GENOVA `IS_discovery` object as created by `insulation_score()`.
`bed`	A `data.frame` with 3 columns in BED format, containing genomic locations for which the insulation score is taken. Alternatively, a `list` of such `data.frame`.
`bed_pos`	A `character` vector of length 1 containing either `"start"`, `"end"` or `"center"` indicating what position of the '`bed`' argument to center insulation scores around.
`region_width`	A `numeric` vector of length 1 for the size in basepairs around the feature to retrieve insulation scores for.
`sort_bins`	A `integer` of length 1 indicating how many central bins should be used to sort the heatmap.
`sort_on`	A `integer` of length 1 noting an experiment on which to sort the heatmap.
`mode`	A `character` of length 1 containing either `"heatmap"`, `"profile"` or `"both"` for how the data should be plotted.
`colour_lim`	A `numeric` vector of length 2 indicating the limits of the heatmap colour scale in insulation scores.
`colours`	A vector of valid colours for the heatmap gradient. Internally defaults to a blue-white-red gradient.
`profile_fun`	A `function` with which to calculate the profile. Should return 1 value per call.
`custom_fill_scale`	A call to one of ggplot2's `scale_fill_*` family of functions to use as the heatmap's scale. If this argument is not `NULL`, it overrides the '`colour_lim`' and '`colour`' arguments.
`profile_ylim`	A `numeric` of length 2 indicating limits for the y-axis in the profile part.
`title`	A `character` or `expression` of length 1 to use as text for the plot title.

Details

The profile colours are automatically assumed from the colours given to the contacts object during the load_contacts operation. Entries in the 'bed' argument that contain > 1 percent missing data are dropped.

Value

A ggplot object.

Examples

## Not run: 
# Calculating insulation scores
ins <- tornado_insulation(list(WT_20kb, KO_20kb), window = 25)

# Calling TADs from the insulation score
tadlist <- call_TAD_insulation(ins)

# Plotting a heatmap
tornado_insulation(ins, tadlist$WT_20kb)

## End(Not run)

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.