plotPeakOrientations: Plot distribution of qualitative peak positions relative to...

In fuscada2/PeakMapper: Flexible Mapping of Genomic Coordinates to Nearest Features

Description

Given a mapping of peaks returned by mapPeaks, plots the qualitative distribution of relative peak locations to their closest feature(s), as classified by mapPeaks. These locations are categorical classifications based on how peaks are located upstream or downstream to their closest feature. Note that if a peak has multiple closest features (e.g. in the case of overlaps), the relative position to each feature will be included in the plot.

Usage

plotPeakOrientations(mappingResult, plotColor = "red",
  mainTitle = "Position of peaks relative to closest features",
  xTitle = "Relative peak position",
  yTitle = "Number of peak-feature pairs",
  backgroundStyle = "blackAndWhite")

Arguments

mappingResult	A dataframe returned by mapPeaks giving the nearest feature(s) to each peak. Format of the dataframe is peak information, followed by feature information, followed by peak position and distance relative to feature, and percent of feature overlapped by peak (see documentation for mapPeaks for more details).
plotColor	The color of the bars on the resulting plot
mainTitle	The main title of the resulting plot
xTitle	The x-axis title of the resulting plot
yTitle	The y-axis title of the resulting plot
backgroundStyle	The style of the plot background. This must be one of either "grey" (for a grey-panelled background), "blackAndWhite" (for a white-panelled background), or "minimal" (for a background with no panelling).

Value

A bar plot giving the distribution of relative peak positions for every mapped peak-feature pair given in mappingResult. The 6 possible classifications for relative peak position are:

• "Downstream (no overlap)" - the peak is downstream of the feature but does not overlap it

• "Overlap (downstream)" - the peak overlaps with the feature and also extends downstream of the feature, but not upstream

• "Overlap (upstream and downstream)" - the feature is contained entirely within the peak

• "Overlap (upstream)" - the peak overlaps with the feature and also extends upstream of the feature, but not downstream

• "Overlap (within feature only)" - the peak is contained entirely with the feature

• "Upstream (no overlap)" - the peak is upstream of the feature but does not overlap it

Examples

## Not run: 
  mappingResult <- mapPeaks(H3K27me3Peaks, WS263Genes)
  plotPeakOrientations(mappingResult)

## End(Not run)

fuscada2/PeakMapper documentation built on Dec. 8, 2019, 12:35 p.m.