Package: patternize 0.0.5

patternize: Quantification of Color Pattern Variation

Quantification of variation in organismal color patterns as obtained from image data. Patternize defines homology between pattern positions across images either through fixed landmarks or image registration. Pattern identification is performed by categorizing the distribution of colors using RGB thresholds or image segmentation.

Authors:Steven Van Belleghem [aut, cre]

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patternize.pdf |patternize.html✨
patternize/json (API)

# Install 'patternize' in R:

install.packages('patternize', repos = c('https://stevenvb12.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stevenvb12/patternize/issues

Datasets:

imageList - ImageList
landmarkArray - LandmarkArray
landmarkList - LandmarkList
rasterList_lanK - RasterList_lanK
rasterList_lanRGB - RasterList_lanRGB
rasterList_regK - RasterList_regK
rasterList_regRGB - RasterList_regRGB

On CRAN:

36 exports 30 stars 2.77 score 102 dependencies 2 mentions 29 scripts 325 downloads

Last updated 3 months agofrom:3f55d2829c. Checks:OK: 1 WARNING: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 24 2024
R-4.5-win	WARNING	Aug 24 2024
R-4.5-linux	WARNING	Aug 24 2024
R-4.4-win	WARNING	Aug 24 2024
R-4.4-mac	WARNING	Aug 24 2024

Exports:alignLan alignReg colorChecker colorChecker_customGray colorChecker_half createPhenotype createTarget GMMImage kImage kImageHSV lanArray makeList maskOutline patArea patGMM patK patK_HSV patLanHSV patLanK patLanK_HSV patLanRGB patLanW patPCA patRDA patRegHSV patRegK patRegK_HSV patRegRGB patRegW plotHeat plotRasterstackAsImage redRes sampleLandmarks sampleRGB setMask sumRaster

Dependencies:abind ape base64enc bezier bmp bslib cachem class classInt cli cluster ClusterR codetools colorRamps colorspace cpp11 DBI digest doParallel downloader dplyr e1071 evaluate fansi farver fastmap fontawesome foreach fs generics geomorph ggplot2 glue gmp gtable highr htmltools htmlwidgets igraph imager isoband iterators jpeg jquerylib jsonlite KernSmooth knitr labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime Morpho munsell nlme ore permute pillar pkgconfig png proxy purrr R6 rappdirs raster RColorBrewer Rcpp RcppArmadillo RcppEigen readbitmap rgl rlang rmarkdown RNifti RNiftyReg RRPP Rvcg s2 sass scales sf sp stringi stringr terra tibble tidyselect tiff tinytex units utf8 vctrs vegan viridisLite withr wk xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Align images using landmarks	alignLan
Aligns images using 'niftyreg' utilities for automated image registration..	alignReg
Calibrate images using ColorChecker.	colorChecker
Calibrate images using ColorChecker.	colorChecker_customGray
Calibrate images using (right) half of ColorChecker. Only works for X-Rite.	colorChecker_half
Plot color pattern prediction for specified PCA values	createPhenotype
Create a target image (RasterStack) from a polygon.	createTarget
External patternize data	extdata
'GMM' clustering of image imported as a RasterStack.	GMMImage
imageList	imageList
'kmeans' clustering of image imported as a RasterStack. This function is used by 'patLanK' and 'patRegK'.	kImage
'kmeans' clustering of image imported as a RasterStack. This function is used by 'patLanK' and 'patRegK'.	kImageHSV
Build landmark array for 'Morpho'.	lanArray
landmarkArray	landmarkArray
landmarkList	landmarkList
Build list of landmarks or RasterStacks from images using filepath and file extension.	makeList
Intersects a RasterStack with an outline. Everything outside of the outline will be removed from the raster.	maskOutline
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.	patArea
Extract colors using GMM clustering (for pre-aligned images).	patGMM
Extract colors using k-means clustering (for pre-aligned images).	patK
Extract colors using k-means clustering (for pre-aligned images).	patK_HSV
Aligns images usings transformations obtained from fixed landmarks and extracts colors using a predefined RGB values and cutoff value.	patLanHSV
Aligns images usings transformations obtained from fixed landmarks and extracts colors using k-means clustering.	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 a predefined RGB values and cutoff value.	patLanRGB
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.	patLanW
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.	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 constrained Redundancy Analysis (RDA) ('rda'). This function also allows to plot the analysis including a visualization of the shape changes along the axis.	patRDA
Aligns images using 'niftyreg' utilities for automated image registration and extracts colors using a predefined HSV values and cutoff value.	patRegHSV
Aligns images using 'niftyreg' utilities for automated image registration and extracts colors using k-means clustering.	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 a predefined RGB values and cutoff value.	patRegRGB
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.	patRegW
patternize - An R package for quantifying color pattern variation.	patternize-package patternize
Plots the color pattern heatmaps from 'sumRaster' output.	plotHeat
Plot rasterStack as image.	plotRasterstackAsImage
rasterList_lanK	rasterList_lanK
rasterList_lanRGB	rasterList_lanRGB
rasterList_regK	rasterList_regK
rasterList_regRGB	rasterList_regRGB
Reduce the resolution of an image imported as a RasterStack by downsampling.	redRes
Sample landmarks in an image.	sampleLandmarks
Interactive function to sample RGB value from pixel or square area in an image.	sampleRGB
Interactive function to to draw an outline for masking.	setMask
This function sums the individual color pattern RasterLayes as obtained by the main patternize functions.	sumRaster