plot.sharpr2: plot.sharpr2

In sharpr2: Estimating Regulatory Scores and Identifying ATAC-STARR Data

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 class '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

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)

sharpr2 documentation built on May 2, 2019, 2:45 p.m.