patternize: patternize - An R package for quantifying color pattern...

In StevenVB12/patternize: Quantification of Color Pattern Variation

patternize - An R package for quantifying color pattern variation.

Description

Quantifying variation in color patterns to study and compare the consistency of their expression necessitates the homologous alignment and color-based segmentation of images. Patternize is an R package that quantifies variation in color patterns as obtained from image data. Patternize defines homology between pattern positions across specimens either through fixed landmarks or image registration. Pattern identification is performed by categorizing the distribution of colors using either an RGB threshold or an unsupervised image segmentation. The quantification of the color patterns can be visualized as heat maps and compared between sets of samples.

patternize main functions

The package has six main functions depending on how you want the alignment of the iamges and the color extraction to be performed.

patLanRGB
Aligns images by transformations obtained from fixed landmarks and extracts colors using a predefined RGB values and cutoff value.

patLanK
Aligns images by transformations obtained from fixed landmarks and extracts colors using k-means clustering.

patLanW
Aligns images by transformations obtained from fixed landmarks and extracts color patterns by watershed segmentation using imager utilities.

patRegRGB
Aligns images using niftyreg utilities for automated image registration and extracts colors using a predefined RGB values and cutoff value.

patRegK
Aligns images using niftyreg utilities for automated image registration and extracts colors using k-means clustering.

patRegW
Aligns images using niftyreg utilities for automated image registration and extracts color patterns by watershed segmentation using imager utilities.

patternize preprocessing functions

The input for the main patternize functions are RasterStack objects and when landmark transformation is used, landmark arrays.

makeList
This function returns a list of RasterStacks or a list of landmarks depending on the input provided.

sampleLandmarks
Sample landmarks in an image.

lanArray
This function creates a landmark array as used by procSym in the package Morpho.

patternize postprocessing functions

sumRaster
This function sums the individual color pattern rasters as obtained by the main patternize functions.

plotHeat
Plots the color pattern heatmaps from sumRaster output.

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.

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). This function also allows to plot the analysis including a visualization of the shape changes along the axis.

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.

patternize miscellaneous functions

redRes
Reduces the resolution of the RasterStack objects to speed up analysis.

kImage
Performs k-means clustering of images.

sampleRGB
Interactive function to sample RGB value from pixel or area in an image.

createTarget
Creates an artificial target images using a provided outline that can be used for image registration (experimantal).

maskOutline
Intersects a RasterStack with an outline. Everything outside of the outline will be removed from the raster.

colorChecker
Calibrate images using ColorChecker.

Author(s)

Steven M. Van Belleghem

See Also

raster, stack, procSym, computeTransform, niftyreg imager

Jon Clayden, Marc Modat, Benoit Presles, Thanasis Anthopoulos and Pankaj Daga (2017). RNiftyReg: Image Registration Using the 'NiftyReg' Library. R package version 2.5.0. https://CRAN.R-project.org/package=RNiftyReg

Stefan Schlager (2016). Morpho: Calculations and Visualisations Related to Geometric Morphometrics. R package version 2.4.1.1. https://github.com/zarquon42b/Morpho

Simon Barthelmé (2017). imager: Image processing library based on ‘CImg’. R package version 0.40.2. https://CRAN.R-project.org/package=imager

StevenVB12/patternize documentation built on Nov. 2, 2023, 8:01 p.m.