patternMap {MPFE} | R Documentation |
Plot the observed distribution and the estimated distribution of the methylation patterns
patternMap(patterns, minFreq=0, maxFreq=1, noSpurious=TRUE, estimatedDistribution=TRUE, topDown=TRUE, allTicks=FALSE, methCol='black', unMethCol='white', ...)
patterns |
A data frame obtained from the output of the function |
minFreq |
Only plot patterns with at least |
maxFreq |
Only plot patterns with more |
noSpurious |
Don't plot spurious patterns (only relevant if |
estimatedDistribution |
Use the frequencies from the estimated distribution. If |
topDown |
Put the most abundant patterns at the top. If |
allTicks |
Draw a tick under every position. |
methCol |
The colour for the methylated positions. Can be a single colour, a vector of colours (recycled), or a function (for instance from |
unMethCol |
As |
... |
Other arguments passed to |
This function draws a map of the different pattern and their frequencies based on the values returned by estimatePatterns
.
Peijie Lin, Sylvain Foret, Conrad Burden
data(patternsExample) estimates <- estimatePatterns(patternsExample, epsilon=0.02, eta=0.01) patternMap(estimates[[1]])