ctPlotSummaryProfiles: ctPlotSummaryProfiles

In jrboyd/seqtsne: Application of t-sne to NGS Genomic Signal Profiles

ctPlotSummaryProfiles

Description

ctPlotSummaryProfiles

Usage

ctPlotSummaryProfiles(
  sts,
  feature_name = NULL,
  signal_name = NULL,
  xbins = 10,
  ybins = xbins,
  profile_value = ssvQC:::val2var[sts$signal_config$plot_value],
  profile_value_label = ssvQC:::val2lab[sts$signal_config$plot_value],
  xrng = NULL,
  yrng = NULL,
  ylim = c(0, NA),
  ma_size = 2,
  n_splines = 10,
  p = NULL,
  N_floor = 0,
  N_ceiling = NULL,
  min_fraction = 0.2,
  return_data = FALSE,
  extra_vars = c("name", "name_split")
)

Arguments

sts	A ChIPtSNE object with ssvQC.prepSignal already called.
feature_name	Feature name present in sts. With default of NULL, first feature name will be used.
signal_name	Signal name present in sts. With default of NULL, first signal name will be used.
xbins	Number of bins (pixel) in the x direction
ybins	Number of bins (pixel) in the y direction. Default reuses xbins.
profile_value	Value to use for profiles. Default is the plot_value defined in the signal config of sts.
profile_value_label	Label to use for profile scale. Default is the plot_value label defined in the signal config of sts.
xrng	numeric vector of length 2 defining range of x-axis. Default is full range.
yrng	numeric vector of length 2 defining range of y-axis. Default is full range.
ylim	Range of y-axis within profile glyphs. Default is 0 to max.
ma_size	Number of profile x-values to use for moving average.
n_splines	Number of splines to use to smooth after moving average.
p	Previous ggplot to plot over.
N_floor	Profiles with N_floor points will have the minimum size.
N_ceiling	Profiles with N_ceiling or more points will have the maximum size.
min_fraction	Minimum fraction between N_floor and N_ceiling required to be included. For example 1) if N_floor is 5, and min_fraction is 0, profiles with fewer than 5 points will be omitted 2) if N_ceiling is 25 and min_fraction is 1, all profiles will be plotted at max size and profiles with fewer than 25 points will be dropped 3) N_floor is 5 and N_ceiling is 25 and min_fraction is .5, profiles with 15 points will be half size and profiles will fewer than 15 points will be omitted.
return_data

Value

ggplot where profiles present in bins are summarized by glyphs.

Examples

data(ex_sts)
ctPlotSummaryProfiles(sts)

jrboyd/seqtsne documentation built on Nov. 5, 2022, 6:37 a.m.