gg_overlap_score_summary_vs_fraction: Plots TopDom Overlap Scores and Lengths as a Function of...
In HenrikBengtsson/TopDomStudy: TopDom Study by Segal et al.

Description Usage Arguments Value See Also Examples

Plots TopDom Overlap Scores and Lengths as a Function of Sample Fraction or Bin Size

gg_overlap_score_summary_vs_fraction(
  dataset,
  chromosome,
  bin_size,
  rhos,
  reference_rhos = rep(1/2, times = length(rhos)),
  window_size = 5L,
  nsamples = 50L,
  weights = c("by_length", "uniform"),
  domain_length = NULL,
  signals = c("mean", "test_len_q0.50"),
  rho_lim = c(0, 1/2),
  length_lim = c(0, 2000),
  rel_heights = c(4, 1),
  labels = c("chromosome"),
  line_col = "black",
  fig_path = "figures",
  fig_format = c("png", "pdf"),
  skip = FALSE,
  ...,
  verbose = TRUE
)

gg_overlap_score_summary_vs_bin_size(
  dataset,
  chromosome,
  bin_sizes,
  rho,
  reference_rho = 1/2,
  window_size = 5L,
  nsamples = 50L,
  weights = c("by_length", "uniform"),
  domain_length = NULL,
  signals = c("mean", "test_len_q0.50"),
  bin_size_lim = c(0, max(bin_sizes)),
  length_lim = c(0, 2000),
  rel_heights = c(4, 1),
  labels = c("chromosome"),
  line_col = "black",
  fig_path = "figures",
  fig_format = c("png", "pdf"),
  skip = FALSE,
  ...,
  verbose = TRUE
)

gg_overlap_score_summary_vs_tad_length(
  dataset,
  chromosome,
  bin_sizes,
  rhos,
  reference_rhos = rep(1/2, times = length(rhos)),
  window_size = 5L,
  nsamples = 50L,
  weights = c("by_length", "uniform"),
  domain_length = NULL,
  signals = c("mean", "test_len_q0.50"),
  tad_length_lim = c(0, 2e+06),
  labels = c("chromosome"),
  line_col = "black",
  fig_path = "figures",
  fig_format = c("png", "pdf"),
  skip = FALSE,
  ...,
  verbose = TRUE
)

`dataset`	(character string) The name of the data set.
`chromosome`	(character string) The chromosome to be plotted.
`bin_size, rho, reference_rho`	(numeric) The bin size (bps) or sample fraction (in (0,0.5]) to be plotted.
`rhos`	(numeric vector) The set of fractions (in (0,0.5]) to process.
`reference_rhos`	(numeric vector) The set of fractions (in (0,0.5]) to process.
`window_size`	(integer) The TopDom windows size. Argument passed as `window.size` to `TopDom::TopDom()`.
`nsamples`	(integer) Number of random samples for produce.
`weights`	(character string) A character string specifying how overlap scores across domains should be weighted. Argument passed as is to `overlap_score_summary()`.
`domain_length`	(optional; character string or numeric vector of length two) If specified, controls how to filter out too short or too long TopDom domains. Argument passed as is to `overlap_score_summary()`.
`signals`	(character vector of length two) The two signals to be plotted in the top and bottom panels.
`rho_lim, bin_size_lim`	The range of the fraction or bin size to be displayed.
`length_lim`	The range of the domain lengths to be displayed.
`rel_heights`	(numeric vector of length two) The relative height of the two figures. Passed to cowplot::plot_grid as is.
`labels`	(character vector). Enable or disable some labels.
`line_col`	The color of the profile curve.
`fig_path`	If non-NULL, an image file is written to this path.
`fig_format`	Image format used for image files.
`skip`	If TRUE and the image file already exists, then it is not replotted.
`verbose`	(logical) If `TRUE`, verbose output is produced.
`bin_sizes`	(numeric vector) The set of bin sizes (in bps) to process.
`tad_length_lim`	The range of the TAD lengths to be displayed.
`...`	Not used.

A ggplot2::ggplot object.

Internal, overlap_score_summary_grid() is used to calculate overlap scores over (chromosome, bin_size, rho).

## These calls with produce folders in the working directory

gg1 <- gg_overlap_score_summary_vs_fraction(
  dataset       = "human,HAP1",
  chromosome    = "22",
  bin_size      = 100*1e3,
  rhos          = c(0.10, 0.20, 0.30, 0.40, 0.50),
  window_size   = 5L,
  weights       = "uniform",
  domain_length = NULL,
  nsamples      = 4L,
  line_col      = "red",
  verbose       = TRUE
)
print(gg1)

gg2 <- gg_overlap_score_summary_vs_bin_size(
  dataset       = "human,HAP1",
  chromosome    = "22",
  bin_sizes     = c(20, 40, 60, 80, 100)*1e3,
  rho           = 0.50,
  window_size   = 5L,
  weights       = "uniform",
  domain_length = NULL,
  nsamples      = 4L,
  line_col      = "blue",
  verbose       = TRUE
)
print(gg2)