R: Quantification of Color Pattern Variation

# Quantification of Color Pattern Variation

## Documentation for package ‘patternize’ version 0.0.5

- DESCRIPTION file
- Package README

## Help Pages

patternize-package | patternize - An R package for quantifying color pattern variation.
alignLan | Align images using landmarks
alignReg | Aligns images using 'niftyreg' utilities for automated image registration..
colorChecker | Calibrate images using ColorChecker.
colorChecker_customGray | Calibrate images using ColorChecker.
colorChecker_half | Calibrate images using (right) half of ColorChecker. Only works for X-Rite.
createPhenotype | Plot color pattern prediction for specified PCA values
createTarget | Create a target image (RasterStack) from a polygon.
extdata | External patternize data
GMMImage | 'GMM' clustering of image imported as a RasterStack.
imageList | imageList
kImage | 'kmeans' clustering of image imported as a RasterStack. This function is used by 'patLanK' and 'patRegK'.
kImageHSV | '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.
patGMM | Extract colors using GMM clustering (for pre-aligned images).
patK | Extract colors using k-means clustering (for pre-aligned images).
patK_HSV | Extract colors using k-means clustering (for pre-aligned images).
patLanHSV | Aligns images usings transformations obtained from fixed landmarks and extracts colors using a predefined RGB values and cutoff value.
patLanK | Aligns images usings transformations obtained from fixed landmarks and extracts colors using k-means clustering.
patLanK_HSV | 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.
patLanW | Extracts color pattern from landmark transformed image using watershed segmentation. This function works interactively by allowing to pick a starting pixel within each pattern element from which the watershed will extract the pattern. This function works best for patterns with sharp boundaries.
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.
patRDA | 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 constrained Redundancy Analysis (RDA) ('rda'). This function also allows to plot the analysis including a visualization of the shape changes along the axis.
patRegHSV | Aligns images using 'niftyreg' utilities for automated image registration and extracts colors using a predefined HSV values and cutoff value.
patRegK | Aligns images using 'niftyreg' utilities for automated image registration and extracts colors using k-means clustering.
patRegK_HSV | 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.
patRegW | Aligns images using 'niftyreg' utilities for automated image registration and extracts color pattern using watershed segmentation. This function works interactively by allowing to pick a starting pixel within each pattern element from which the watershed will extract the pattern. This function works best for patterns with sharp boundaries.
patternize | patternize - An R package for quantifying color pattern variation.
plotHeat | Plots the color pattern heatmaps from 'sumRaster' output.
plotRasterstackAsImage | Plot rasterStack as image.
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.
sampleLandmarks | Sample landmarks in an image.
sampleRGB | Interactive function to sample RGB value from pixel or square area in an image.
setMask | Interactive function to to draw an outline for masking.
sumRaster | This function sums the individual color pattern RasterLayes as obtained by the main patternize functions.