plotAverageProfile {epistack}R Documentation

plotAverageProfile()

Description

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

Usage

plotAverageProfile(
  gr,
  pattern = "^window_",
  x_labels = c("Before", "Anchor", "After"),
  palette = colorRampPalette(c("magenta", "black", "green")),
  alpha_for_se = 0.25,
  error_type = c("sd", "sem"),
  reversed_z_order = FALSE,
  ylim = NULL
)

Arguments

gr

a GRanges input

pattern

a single character that should match metadata of gr (can be a regular expression).

x_labels

x-axis labels.

palette

a color palette function, by default: colorRampPalette(c("magenta", "black", "green"))

alpha_for_se

the transparency (alpha) value for the error band.

error_type,

can be either sd (standard deviation) or sem (standard error of the mean). Default: sem.

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

Value

Display a plot.

Examples

data("stackepi")
plotAverageProfile(stackepi)


[Package epistack version 1.0.0 Index]