plotPairsProbabilityMatrix: Plots a matrix of base pair probabilities

In ncRNAtools: An R toolkit for non-coding RNA

Description

Generates a heatmap-like plot to visualize the probabilities that different bases of an RNA molecule form a pair.

Usage

plotPairsProbabilityMatrix(basePairProbsMatrix, probabilityThreshold=0.1,
                           colorPalette=paste(rainbow(7, rev=TRUE), "FF", sep=""))

Arguments

basePairProbsMatrix	A symmetric square matrix containing the probabilities of pairs between different bases. Should be in the same format as output by the generatePairsProbabilityMatrix function.
probabilityThreshold	Threshold for representing the probability that two given bases form a pair. Pairs with a probability lower than the threshold will not be considered, and their corresponding cell in the plot will be left blank.
colorPalette	Color palette to be used for displaying the probabilities above the specified threshold.

Value

A ggplot object with a representation of the base pair probability matrix.

Examples

# Load an example table of base pair probabilities, calculated with centroidFold:

basePairProbabilitiesTable <- read.csv(system.file("extdata", 
"exampleBasePairProbabilitiesTable.csv", package="ncRNAtools"))

# Generate a matrix of base pair probabilities:

probabilitiesMatrix <- generatePairsProbabilityMatrix(basePairProbabilitiesTable)

# Plot the probability matrix

plotPairsProbabilityMatrix(probabilitiesMatrix)

ncRNAtools documentation built on Nov. 8, 2020, 8:14 p.m.