Description Usage Arguments Value See Also Examples
Plots TopDom Overlap Scores and Lengths as a Function of Sample Fraction or Bin Size
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | 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 |
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 |
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 |
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 |
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).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ## 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.