ssvSignalLineplot: construct line type plots where each region in each sample is...

In seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

Description

construct line type plots where each region in each sample is represented

Usage

ssvSignalLineplot(
  bw_data,
  x_ = "x",
  y_ = "y",
  color_ = "sample",
  sample_ = "sample",
  region_ = "id",
  group_ = "auto_grp",
  line_alpha = 1,
  facet_ = "auto_facet",
  facet_method = facet_wrap,
  spline_n = NULL,
  return_data = FALSE
)

Arguments

bw_data	a GRanges or data.table of bigwig signal. As returned from ssvFetchBam and ssvFetchBigwig
x_	variable name mapped to x aesthetic, x by default.
y_	variable name mapped to y aesthetic, y by default.
color_	variable name mapped to color aesthetic, sample by default.
sample_	variable name, along with region_ used to group and facet by default, change group_ or facet_ to override.
region_	variable name, along with sample_ used to group and facet by default, change group_ or facet_ to override.
group_	group aesthetic keeps lines of geom_path from mis-connecting. auto_grp by default which combines sample_ and region_. probably shouldn't change.
line_alpha	alpha value for lines. default is 1.
facet_	facetting divides up plots. auto_facet by default which combines sample_ and region_. if overriding facet_method with facet_grid, make sure to include ~ between two variables, ie. "a~b", ".~b", "a~."
facet_method	ggplot2 facetting method or wrapper for same, facet_wrap by default.
spline_n	if not NULL, applySpline will be called with n = spline_n. default is NULL.
return_data	logical. If TRUE, return value is no longer ggplot and is instead the data used to generate that plot. Default is FALSE.

Value

ggplot of signal potentially facetted by region and sample

Examples

bw_gr = CTCF_in_10a_profiles_gr
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)), facet_ = "sample")
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)),
    facet_ = "sample~.",
    facet_method = facet_grid)
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)),
    facet_ = paste("sample", "~", "id"), facet_method = facet_grid)
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)))
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)), facet_ = "id")
ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)),
    facet_ = "id", spline_n = 10)

seqsetvis documentation built on Nov. 8, 2020, 5:57 p.m.