![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| patternize-package | patternize - An R package for quantifying color pattern variation. |
| createTarget | Create a target image (RasterStack) from a polygon. |
| extdata | External patternize data |
| imageList | imageList |
| kImage | 'kmeans' clustering of image imported as a RasterStack. This function is used by 'patLanK' and 'patRegK'. |
| lanArray | Build landmark array for 'Morpho'. |
| landmarkArray | landmarkArray |
| landmarkList | landmarkList |
| makeList | Build list of landmarks or RasterStacks from images using filepath and file extension. |
| maskOutline | Intersects a RasterStack with an outline. Everything outside of the outline will be removed from the raster. |
| patArea | This fucntion calculates the area in which the color pattern is expressed in each sample as the relative proportion using the provided outline of the considered trait or structure. |
| patLanK | Aligns images usings transformations obtained from fixed landmarks and extracts colors using k-means clustering. |
| patLanRGB | Aligns images usings transformations obtained from fixed landmarks and extracts colors using a predefined RGB values and cutoff value. |
| patPCA | This function transforms the individual color pattern rasters as obtained by the main patternize functions to a dataframe of 0 and 1 values that can be used for Principal Component Analysis ('prcomp'). This function also allows to plot the analysis including a visualization of the shape changes along the axis. Pixel values are predicted by multiplying the rotation matrix (eigenvectors) with a vector that has the same length as the number of rows in the rotation matrix and in which all values are set to zero except for the PC value for which we want to predict the pixel values. |
| patRegK | Aligns images using 'niftyreg' utilities for automated image registration and extracts colors using k-means clustering. |
| patRegRGB | Aligns images using 'niftyreg' utilities for automated image registration and extracts colors using a predefined RGB values and cutoff value. |
| patternize | patternize - An R package for quantifying color pattern variation. |
| plotHeat | Plots the color pattern heatmaps from 'sumRaster' output. |
| rasterList_lanK | rasterList_lanK |
| rasterList_lanRGB | rasterList_lanRGB |
| rasterList_regK | rasterList_regK |
| rasterList_regRGB | rasterList_regRGB |
| redRes | Reduce the resolution of an image imported as a RasterStack by downsampling. |
| sumRaster | This function sums the individual color pattern RasterLayes as obtained by the main patternize functions. |