addLabel | Plot a label with optional polygon background |
addLineBackToOriginalLocation | Plot line from new alternative location back to original |
addPlottedLabel | Add the information associated with a text label that has... |
addPoints | Add non-overlapping points to plot |
addSNPScale | Add a SNP scale to phylogeny |
addTextLabels | Add non-overlapping text labels to plot |
calculateAxesCoordinatesAtEachLevel | Define the coordinates for the radar level labels |
calculateLabelHeightsAndWidths | Calculate the heights and widths of the labels in the current... |
calculateLocation | Get the X and Y coordinates of a string coded location on a... |
calculatePointShapeSize | A function to calculate the size of a point shape in the... |
calculatePointSize | Calculate the size of a point on the current plot |
calculateWatermarkCex | Calculate the factor to multiple text by so that it fits to... |
calculateYAxisLimits | Calculate the limits of the Y axis |
checkAlignmentClass | Count the number of different nucleotides at a position in a... |
chooseNewLocation | A function to choose (from the alternative locations) a new... |
countNucleotidesAtSite | Count the number of different nucleotides at a position in a... |
createHistogramObjects | Create, but don't plot, a histogram for each distribution |
defineBreaks | Define the breaks to be used in histograms |
euclideanDistance | Calculate the euclidean distance between two points |
euclideanDistancesWithRescaledXAxis | Calculate the euclidean distance between two sets of points.... |
generateAlternativeLocations | Generate a set of alternative locations where labels can be... |
generateEquiDistantPointsOnCircle | Generate equidistant points on a circle |
generatePointsAlongPolygon | Places set number of points along the edges of a polygon. |
identifyValuesInBins | A function used to identify the indices of the values falling... |
identifyWhiskersAndOutliers | A function to identify the locations of the whiskers in a... |
outsidePlot | Checks whether adding a label at the current point will... |
overlapsWithPlottedPoints | Checks whether a point is too close to any of the plotted... |
plotBinBoundaries | A function used in development to see the size of the bins... |
plotFASTA | Plot the different nucleotides present in an alignment of... |
plotMultipleHistograms | Plot multiple histograms in the same plot |
progress | A progress bar function to run within a 'for' loop |
radarChart | A function to produce a radar chart designed for mapping... |
removeLocationAndThoseCloseToItFromAlternatives | Remove coordinates of alternative locations that are too... |
removeNAValues | Remove 'NA' values from each distribution |
setAlpha | A progress bar function to run within a 'for' loop |
setOption | A function to assign value if multiple options are available,... |
spreadPoints | Add spreaded, to avoid overlap, points to a boxplot |
spreadPointsMultiple | Add spreaded, to avoid overlap, points to a boxplot... |
testPchSizeCalculator | A function used in development to see how well the size of a... |
tooClose | Checks whether a point is too close to any of the plotted... |
watermark | Add a watermark to an existing plot |
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