plotPairsProbabilityMatrix {ncRNAtools} | R Documentation |
Generates a heatmap-like plot to visualize the probabilities that different bases of an RNA molecule form a pair.
plotPairsProbabilityMatrix(basePairProbsMatrix, probabilityThreshold=0.1, colorPalette=paste(rainbow(7, rev=TRUE), "FF", sep=""))
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. |
A ggplot object with a representation of the base pair probability matrix.
# 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)