Man pages for JosephCrispell/plotteR
A collection of functions to help with base R plotting
| 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 |
