ssvSignalBandedQuantiles: plot profiles from bigwigs

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

plot profiles from bigwigs

Description

plot profiles from bigwigs

Usage

ssvSignalBandedQuantiles(
  bw_data,
  y_ = "y",
  x_ = "x",
  by_ = "fake",
  hsv_reverse = FALSE,
  hsv_saturation = 1,
  hsv_value = 1,
  hsv_grayscale = FALSE,
  hsv_hue_min = 0,
  hsv_hue_max = 0.7,
  hsv_symmetric = FALSE,
  n_quantile = 18,
  quantile_min = 0.05,
  quantile_max = 0.95,
  return_data = FALSE
)

Arguments

bw_data	a GRanges or data.table of bigwig signal. As returned from ssvFetchBam and ssvFetchBigwig
y_	the variable name in bw_data for y axis in plot
x_	the variable name in bw_data for x axis in plot
by_	the variable name in bw_data to facet on
hsv_reverse	logical, should color scale be reversed? default FALSE
hsv_saturation	numeric value from 0 to 1. Saturation for color scale. default 1
hsv_value	numeric value from 0 to 1. Value for color scale. default 1
hsv_grayscale	logical, if TRUE gray() is used instead of rainbow(). default FALSE
hsv_hue_min	numeric [0, hsv_hue_max) hue min of color scale
hsv_hue_max	numeric (hsv_hue_min, 1] hue max of color scale
hsv_symmetric	if TRUE, colorscale is symmetrical, default FALSE.
n_quantile	number of evenly size quantile bins
quantile_min	the lowest quantile start
quantile_max	the highest quantile end
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 object using ribbon plots to show quantile distributions

Examples

data(CTCF_in_10a_profiles_gr)
#rainbow colors
qgr = CTCF_in_10a_profiles_gr
ssvSignalBandedQuantiles(qgr)
#grayscale
ssvSignalBandedQuantiles(qgr, hsv_grayscale = TRUE,
    hsv_symmetric = TRUE, hsv_reverse = TRUE)
#using "by_" per sample
ssvSignalBandedQuantiles(qgr, hsv_grayscale = TRUE,
    hsv_symmetric = TRUE, hsv_reverse = TRUE, by_ = "sample")
#adding spline smoothing
splined = applySpline(qgr, n = 10,
    by_ = c("id", "sample"))
ssvSignalBandedQuantiles(splined, n_quantile = 50,
    quantile_min = .25, quantile_max = .75,
    hsv_symmetric = TRUE, hsv_reverse = TRUE, by_ = "sample")

jrboyd/seqsetvis documentation built on June 1, 2024, 5:39 a.m.