noiseComparisonPlot: Creates a metaplot for comparing noise analysis results with...

In Bishop-Laboratory/RLSeq: RLSeq: An analysis package for R-loop mapping data

Creates a metaplot for comparing noise analysis results with RLBase

Description

Plots the average standardized signal from noiseAnalyze alongside the samples in RLBase. For this plot, lower average signal indicates better signal to noise ratio. Note: This plot may be misleading if you supplied custom windows when running noiseAnalyze.

Usage

noiseComparisonPlot(object, mode = "auto", simple = TRUE, returnData = FALSE)

Arguments

object	An RLRanges object with noiseAnalyze already run.
mode	A character containing the R-loop data mode to compare against. See details for more information.
simple	A logical which specifies whether the plot should only show samples where the prediction and label are the same. Default: TRUE.
returnData	If TRUE, plot data is returned instead of plotting. Default: FALSE

Details

Mode

The mode parameter specifies the R-loop modality to compare the user-supplied sample against in the plot. The default, "auto" specifies that the mode from the supplied RLRanges object will be used. Only one mode can be specified. For a list of applicable modes, see auxdata$available_modes.

Plot

The plot is a violin / jitter plot showing the distribution of average values from the noiseAnalyze output across RLBase samples of the selected mode. The user-supplied sample is annotated on the plot.

Value

A ggplot2::ggplot object or a tbl if returnData is TRUE.

Examples

rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq"))

# Plot RL-Region overlap
noiseComparisonPlot(rlr)

# Return data only
noiseComparisonPlot(rlr, returnData = TRUE)

Bishop-Laboratory/RLSeq documentation built on Jan. 28, 2023, 11:38 p.m.