Quantification of Color Pattern Variation

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Documentation for package ‘patternize’ version 0.0.5

• DESCRIPTION file.

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.