ssvSignalBandedQuantiles: plot profiles from bigwigs

Description Usage Arguments Value Examples

View source: R/functions_signal_plots.R

Description

plot profiles from bigwigs

Usage

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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 [0, 1] saturation for color scale. default 1

hsv_value

numeric [0, 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

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#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")

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