plotTxFeatureOverlap: Plot Transcript Feature Overlap

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

Plot Transcript Feature Overlap

Description

Plots the results of txFeatureOverlap alongside the average from public R-loop datasets. This allows comparison of user-supplied samples with data that is expected to be simialr.

Usage

plotTxFeatureOverlap(object, mode = "auto", returnData = FALSE)

Arguments

object	An RLRanges object with txFeatureOverlap already run.
mode	A character containing the R-loop data mode to compare against. See details for more information.
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 stacked bar chart showing the proportion of peaks overlapping transcript features for the supplied RLRanges object. Additionally, the average of the txFeatureOverlap analysis for all samples within the specified modes are also shown as a background comparison.

This style of analysis enables a user to see the transcript features overlapping their peaks and compare those results to the average within relevant public datasets.

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
plotTxFeatureOverlap(rlr)

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

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