patArea {patternize}

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)