patRDA {patternize} | 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.
See Also
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)