ctPlotBinAggregates: ctPlotBinAggregates

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

ctPlotBinAggregates

Description

Divide t-SNE space into xbins*ybins and summarize signal in each bean as the mean value results from agg_FUN on xmin:xmax of signal profiles present.

Usage

ctPlotBinAggregates(
  sts,
  feature_name = NULL,
  signal_name = NULL,
  xmin = -Inf,
  xmax = Inf,
  profile_value = ssvQC:::val2var[sts$signal_config$plot_value],
  profile_value_label = ssvQC:::val2lab[sts$signal_config$plot_value],
  agg_FUN = max,
  xbins = 50,
  ybins = xbins,
  bg_color = "gray60",
  min_size = 5,
  extra_vars = character()
)

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.
xmin	The min range of x-values to apply agg_FUN to.
xmax	The max range of x-values to apply agg_FUN to.
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.
agg_FUN	A function appled to all y_ values in xmin to xmax range. Must accept single numeric vector and return 1 value.
xbins	Number of bins (pixel) in the x direction
ybins	Number of bins (pixel) in the y direction. Default reuses xbins.
bg_color	Color to use for plot background. Default is "gray60".
min_size	Bins must contain at least this many points to appear in final plot.

Value

ggplot summarizing signal profiles across t-SNE space in heatmap style plot.

Examples

data(ex_sts)
ctPlotBinAggregates(sts)

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