ssvSignalBandedQuantiles {seqsetvis}R Documentation

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)

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

Value

ggplot object using ribbon plots to show quantile distributions

Examples

#rainbow colors
ssvSignalBandedQuantiles(CTCF_in_10a_profiles_gr)
ssvSignalBandedQuantiles(CTCF_in_10a_profiles_gr, hsv_symmetric = TRUE,
    hsv_reverse = TRUE)
#grayscale
ssvSignalBandedQuantiles(CTCF_in_10a_profiles_gr, hsv_grayscale = TRUE)
ssvSignalBandedQuantiles(CTCF_in_10a_profiles_gr, hsv_grayscale = TRUE,
    hsv_symmetric = TRUE, hsv_reverse = TRUE)
#using "by_" per sample
ssvSignalBandedQuantiles(CTCF_in_10a_profiles_gr, hsv_grayscale = TRUE,
    hsv_symmetric = TRUE, hsv_reverse = TRUE, by_ = "sample")
#adding spline smoothing
splined = applySpline(CTCF_in_10a_profiles_gr, 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")

[Package seqsetvis version 1.0.2 Index]