patArea: This fucntion calculates the area in which the color pattern...

In patternize: Quantification of Color Pattern Variation

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.

Description

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.

Usage

patArea(
  rList,
  IDlist,
  refShape,
  type,
  outline = NULL,
  landList = NULL,
  adjustCoords = FALSE,
  cartoonID = NULL,
  crop = c(0, 0, 0, 0),
  flipRaster = NULL,
  flipOutline = NULL,
  imageList = NULL
)

Arguments

rList	List of RasterLayers as obtained from the main patternize functions.
IDlist	List of sample IDs.
refShape	This can be 'target' in case the reference shape is a single sample (for registration analysis) or 'mean' if the images were transformed to a mean shape using landmark transformation.
type	Type of rasterlist; 'RGB' or 'k' (result from RGB or k-means analysis, respectively).
outline	xy coordinates that define outline.
landList	Landmark list as returned by makeList.
adjustCoords	Adjust landmark coordinates in case they are reversed compared to pixel coordinates (default = FALSE).
cartoonID	ID of the sample for which the cartoon was drawn.
crop	Vector c(xmin, xmax, ymin, ymax) that specifies the pixel coordinates to crop the original image used in landmark or registration analysis.
flipRaster	Whether to flip raster along xy axis (in case there is an inconsistency between raster and outline coordinates).
flipOutline	Whether to flip plot along x, y or xy axis.
imageList	List of images as obtained from makeList should be given if one wants to flip the outline or adjust landmark coordinates.

Value

Table or list of tables with sample IDs and relative area of color pattern or kmeans cluster.

Examples

data(rasterList_lanRGB)
#data(rasterList_regRGB)
#data(rasterList_lanK)
#data(rasterList_regK)

data(imageList)

IDlist <- c('BC0077','BC0071','BC0050','BC0049','BC0004')

outline_BC0077 <- read.table(paste(system.file("extdata",  package = 'patternize'),
'/BC0077_outline.txt', sep=''), header = FALSE)

prepath <- system.file("extdata", package = 'patternize')
extension <- '_landmarks_LFW.txt'

landmarkList <- makeList(IDlist, 'landmark', prepath, extension)

## Not run: 
area_lanRGB <- patArea(rasterList_lanRGB, IDlist, refShape = 'mean', type = 'RGB',
outline = outline_BC0077, landList = landmarkList, adjustCoords = TRUE,
imageList = imageList, cartoonID = 'BC0077')

area_regRGB <- patArea(rasterList_regRGB, IDlist, refShape = 'target', type = 'RGB',
outline = outline_BC0077, crop = c(100,400,40,250), adjustCoords = TRUE,
imageList = imageList, cartoonID = 'BC0077', flipRaster = 'xy')

areaList_lanK <- patArea(rasterList_lanK, IDlist, refShape = 'mean', type = 'k',
outline = outline_BC0077, landList = landmarkList, adjustCoords = TRUE,
imageList = imageList, cartoonID = 'BC0077')

areaList_regK <- patArea(rasterList_regK, IDlist, refShape = 'target', type = 'k',
outline = outline_BC0077, crop = c(100,400,40,250), adjustCoords = TRUE,
imageList = imageList, cartoonID = 'BC0077', flipRaster = 'xy')

## End(Not run)

patternize documentation built on Aug. 22, 2023, 5:07 p.m.