sharpr2 (version 1.1.1.0)

plot.sharpr2: plot.sharpr2

Description

Given an object returned from the sharpr2 function, this function plots the estimated scores (with s.e. if available) for a tiled region.

Usage

# S3 method for sharpr2
plot(x, tr, unc = "CI", loess = FALSE, add = FALSE,
  xlab = "Position", ylab = "Regulatory Score", cicol = 'orange', cimcol = 'grey', 
  sreg = TRUE, ...)

Arguments

x

An object returned from the sharpr2 function.

tr

An integer indicating which tiled region to be plotted.

unc

'MSE' or 'CI', indicating whether to plot sqrt(MSE) or 95%CI for uncertainty. The default is 'CI'.

loess

An indicator for whether the loess method is used for smoothing in plotting the scores from sharpr2. The standard errors are not plotted when loess is used.

add

An indicator for whether to add the new plot to the existing one.

xlab

The label for the x-axis. The default is 'Position'.

ylab

The label for the y-axis. The default is 'Regulatory Score'.

cicol

The color for CIs. The default is 'orange'.

cimcol

The color for filling the regions within CIs. The default is 'grey'.

sreg

An indicator for whether to highlight the identified driver element regions. The default is TRUE.

...

Other parameters for plot.

Examples

# NOT RUN {
data(hidra_ex)
re <- sharpr2(hidra_ex[1:2000,], l_min = 150, l_max = 600, f_dna = 5, f_rna = 0, sig=FALSE)
plot(re,584)
# }