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| aacids | properties of amino acids |
| alphabet | alphabet polygon data |
| calcInformation | Compute shannon information based on position and treatment |
| createPolygons | Create a data set of polygons for a set of letters from a specified fontfamily |
| determineOrder | Determine order in which to pass through a set of points |
| fortify | Convert image matrix to a data frame |
| fortify.default | Convert image matrix to a data frame |
| GeomLogo | Sequence logo plots. |
| geom_logo | Sequence logo plots. |
| getOutline | Determine boundary between foreground and background in an image |
| ggfortify | Convert sequence data to a format suitable for logo plots |
| identifyParts | Identify different parts of a polygon |
| letterObject | Convert a text element into an R object |
| letterToPolygon | Convert an image file to a polygon |
| logo | Logo plot |
| mainPlusIslands | Set the orientation of a polygon |
| point_line_dist | Distance between point and line |
| PositionClassic | Logo positioning for overlapping objects on top of one another. |
| PositionLogo | Logo positioning for overlapping objects on top of one another. |
| position_classic | Logo positioning for overlapping objects on top of one another. |
| position_logo | Logo positioning for overlapping objects on top of one another. |
| sequences | peptide sequence data |
| simplifyPolygon | Douglas-Peucker algorithm adjusted fo polyons |
| simplify_rec | Douglas Pecker algorithm for line thinning |
| splitSequence | Reshape data set according to elements in sequences |
| StatLogo | Calculation of all pieces necessary to plot a logo sequence plot |
| stat_logo | Calculation of all pieces necessary to plot a logo sequence plot |