plotAverageProfile: plotAverageProfile()

In GenEpi-GenPhySE/epistack: Heatmaps of Stack Profiles from Epigenetic Signals

plotAverageProfile()

Description

Plot the average stack profiles +/- error (sd or sem). If a bin column is present in rowRanges(rse), one average profile is drawn for each bin.

Usage

plotAverageProfile(
  rse,
  assay = NULL,
  x_labels = c("Before", "Anchor", "After"),
  palette = colorRampPalette(c("#DF536B", "black", "#61D04F")),
  alpha_for_se = 0.25,
  error_type = c("sd", "sem", "ci95"),
  reversed_z_order = FALSE,
  ylim = NULL,
  y_title = NULL,
  pattern = NULL
)

Arguments

rse	a RangedSummarizedExperiment input. Aletrnatively: can be a GRanges object (for backward compatibility, pattern will be required).
assay	specify the name of the assay to plot, that should match one of assayNames(rse).
x_labels	x-axis labels.
palette	A vector of colors, or a function that returns a palette of n colors.
alpha_for_se	the transparency (alpha) value for the error band.
error_type,	can be either "sd" (standard deviation), "sem" (standard error of the mean), or "ci95" (95% confidence interval). Default: "sd".
reversed_z_order	should the z-order of the curves be reversed (i.e. first or last bin on top?)
ylim	a vector of two numbers corresponding to the y-limits of the plot.
y_title	the y-axis title.
pattern	only if rse is of class GRanges. A single character that should match metadata of rse (can be a regular expression).

Value

Display a plot.

Examples

data("stackepi")
plotAverageProfile(stackepi)

GenEpi-GenPhySE/epistack documentation built on July 27, 2023, 1:09 a.m.