patRDA: This function transforms the individual color pattern rasters...
In patternize: Quantification of Color Pattern Variation

patRDA

R Documentation

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.

Description

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.

Usage

patRDA(
  rList,
  popList,
  colList,
  symbolList = NULL,
  rListPredict = NULL,
  popListPredict = NULL,
  colListPredict = NULL,
  symbolListPredict = NULL,
  plot = FALSE,
  plotType = "points",
  plotChanges = FALSE,
  PCx = 1,
  PCy = 2,
  plotCartoon = FALSE,
  refShape = NULL,
  outline = NULL,
  lines = NULL,
  landList = NULL,
  adjustCoords = FALSE,
  crop = c(0, 0, 0, 0),
  flipRaster = NULL,
  flipOutline = NULL,
  imageList = NULL,
  cartoonID = NULL,
  colpalette = NULL,
  normalized = NULL,
  cartoonOrder = "above",
  lineOrder = "above",
  cartoonCol = "gray",
  cartoonFill = NULL,
  plotLandmarks = FALSE,
  landCol = "black",
  zlim = c(-1, 1),
  legendTitle = "Predicted",
  xlab = "",
  ylab = "",
  main = ""
)

Arguments

`rList`	List of raster objects.
`popList`	List of vectors including sampleIDs for each population.
`colList`	List of colors for each population.
`symbolList`	List with graphical plotting symbols (default = NULL).
`rListPredict`	List of raster objects to predict into DFA space (default = NULL).
`popListPredict`	List of vectors including sampleIDs for each set of predict samples (default = NULL). Note to that this also has to be a list if only one population is included.
`colListPredict`	List of colors for each set of predict samples (default = NULL).
`symbolListPredict`	List with graphical plotting symbols for predict sets (default = NULL).
`plot`	Whether to plot the PCA analysis (default = FALSE).
`plotType`	Plot 'points' or sample 'labels' (default = 'points')
`plotChanges`	Wether to include plots of the changes along the PC axis (default = FALSE).
`PCx`	PC axis to be presented for x-axis (default PC1).
`PCy`	PC axis to be presented for y-axis (default PC2).
`plotCartoon`	Whether to plot a cartoon. This cartoon should be drawn on one of the samples used in the analysis.
`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 (only for meanshape when using landmark transformation)
`outline`	xy coordinates that define outline.
`lines`	list of files with xy coordinates of line objects to be added to cartoon.
`landList`	Landmark landmarkList.
`adjustCoords`	Adjust landmark coordinates.
`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 image should be given if one wants to flip the outline or adjust landmark coordinates.
`cartoonID`	ID of the sample for which the cartoon was drawn.
`colpalette`	Vector of colors for color palette (default = c("white","lightblue","blue","green", "yellow","red"))
`normalized`	Set this to true in case the summed rasters are already devided by the sample number.
`cartoonOrder`	Whether to plot the cartoon outline 'above' or 'under' the pattern raster (default = 'above'). Set to 'under' for filled outlines.
`lineOrder`	Whether to plot the cartoon lines 'above' or 'under' the pattern raster (default = 'above').
`cartoonCol`	Outline and line color for cartoon (deafault = 'gray').
`cartoonFill`	Fill color for outline of cartoon (default = NULL).
`plotLandmarks`	Whether to plot the landmarks from the target image or mean shape landmarks (default = FALSE).
`landCol`	Color for plotting landmarks (default = 'black').
`zlim`	z-axis limit (default = c(0,1))
`legendTitle`	Title of the raster legend (default = 'Proportion')
`xlab`	Optional x-axis label.
`ylab`	Optional y-axis label.
`main`	Optional main title.

Value

If plot = TRUE: List including a [1] dataframe of the binary raster values that can be used for discriminant function analysis, [2] a dataframe of sample IDs and specified population colors and [3] lda results. if rListPredict not empty: [4] class prediction of samples. If plot = FALSE: lda result only.

Examples

data(rasterList_lanRGB)

pop1 <- c('BC0077','BC0071')
pop2 <- c('BC0050','BC0049','BC0004')
popList <- list(pop1, pop2)
colList <- c("red", "blue")

pcaOut <- patRDA(rasterList_lanRGB, popList, colList, plot = TRUE)

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