plotEnrichment: Plot Enrichment Test Results

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

Plot Enrichment Test Results

Description

Creates a list of plots, one for each annotation database (see RLHub::annotations). These plots show the feature enrichment for the user-supplied sample in comparison to the samples in RLBase. This will only work if you did not use custom annotations with featureEnrich.

Usage

plotEnrichment(
  object,
  pred_POS_only = TRUE,
  label_POS_only = FALSE,
  splitby = c("none", "prediction", "label"),
  limits = c(-10, 15),
  returnData = FALSE,
  ...
)

Arguments

object	An RLRanges object with featureEnrich already run.
pred_POS_only	If TRUE, only "POS" predicted samples included (see also predictCondition). Default: TRUE.
label_POS_only	If TRUE, only "POS" labeled samples included (samples which are expected to robustly map R-loops, e.g., "D210N" condition R-ChIP data). Default: FALSE.
splitby	Metadata by which to split plots. Can be "none", "prediction", or "label".
limits	Specify limits on data range. This is used for controlling the infinite estimation of odds ratio resulting from fisher's exact test. To remove limits, set c(-Inf, Inf). Default: c(-10, 15).
returnData	If TRUE, plot data is returned instead of plot objects. Default: FALSE
...	For internal use.

Value

A named list of ggplot2::ggplot objects. Names correspond to the annotations provided. See also featureEnrich.

Examples

# Example dataset with featureEnrich() already run.
rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq"))

# Make plots, split by prediction
plotEnrichment(rlr, pred_POS_only = FALSE, splitby = "prediction")

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