plotHeat: Plots the color pattern heatmaps from 'sumRaster' output.

In StevenVB12/patternize: Quantification of Color Pattern Variation

Plots the color pattern heatmaps from sumRaster output.

Description

Plots the color pattern heatmaps from sumRaster output.

Usage

plotHeat(
  summedRaster,
  IDlist,
  colpalette = NULL,
  plotCartoon = FALSE,
  refShape = NULL,
  outline = NULL,
  lines = NULL,
  landList = NULL,
  adjustCoords = FALSE,
  cartoonID = NULL,
  normalized = FALSE,
  crop = c(0, 0, 0, 0),
  flipRaster = NULL,
  flipOutline = NULL,
  imageList = NULL,
  refImage = NULL,
  cartoonOrder = "above",
  lineOrder = "above",
  cartoonCol = "gray",
  cartoonFill = NULL,
  plotLandmarks = FALSE,
  landCol = "black",
  zlim = c(0, 1),
  legend = TRUE,
  legendTitle = "Proportion",
  legend.side = 4,
  xlab = "",
  ylab = "",
  main = "",
  plotType = "multi",
  imageIDs = NULL,
  format = "imageJ"
)

Arguments

summedRaster	Summed raster or summedRasterList.
IDlist	List of sample IDs.
colpalette	Vector of colors for color palette (default = c("white","lightblue","blue","green", "yellow","red"))
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.
cartoonID	ID of the sample for which the cartoon was drawn.
normalized	Set this to true in case the summed rasters are already devided by the sample number.
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 should be given if one wants to flip the outline or adjust landmark coordinates.
refImage	Image (RasterStack) used for target. Use raster::stack('filename').
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 ploting landmarks (default = 'black').
zlim	z-axis limit (default = c(0,1))
legend	Whether to plot legend with heatmaps.
legendTitle	Title of the raster legend (default = 'Proportion')
legend.side	Side to plot legend (default = 4)
xlab	Optional x-axis label.
ylab	Optional y-axis label.
main	Optional main title.
plotType	Set as 'PCA' when visualizing shape changes along PCA axis in \ codepatPCA, as 'one' when visualizing single image or as 'multi' for multi plotting or when setting customized margins (default = 'multi').
imageIDs	A list of IDs to match landmarks to images if landmarkList and imageList don't have the same length.
format	ImageJ (Fiji) or tps format (default = 'imageJ').

Examples

data(rasterList_lanRGB)
IDlist <- c('BC0077','BC0071','BC0050','BC0049','BC0004')
outline_BC0077 <- read.table(paste(system.file("extdata",  package = 'patternize'),
'/BC0077_outline.txt', sep=''), header = FALSE)
lines_BC0077 <- list.files(path=paste(system.file("extdata",  package = 'patternize')),
pattern='vein', full.names = TRUE)

summedRaster_regRGB <- sumRaster(rasterList_regRGB, IDlist, type = 'RGB')
data(imageList)

plotHeat(summedRaster_regRGB, IDlist, plotCartoon = TRUE, refShape = 'target',
outline = outline_BC0077, lines = lines_BC0077, crop = c(100,400,40,250),
flipRaster = 'xy', imageList = imageList, cartoonOrder = 'under', cartoonID = 'BC0077',
cartoonFill = 'black', main = 'registration_example')

## Not run: 
data(rasterList_lanK)
IDlist <- c('BC0077','BC0071','BC0050','BC0049','BC0004')
summedRasterList <- sumRaster(rasterList_lanK, IDlist, type = 'k')
plotHeat(summedRasterList, IDlist)

summedRasterList_regK <- sumRaster(rasterList_regK, IDlist, type = 'k')
plotHeat(summedRasterList_regK, IDlist, plotCartoon = TRUE, refShape = 'target',
outline = outline_BC0077, lines = lines_BC0077, crop = c(100,400,40,250),
flipRaster = 'y', imageList = imageList, cartoonOrder = 'under',
cartoonFill = 'black', main = 'kmeans_example')

plotHeat(summedRasterList_regK[[1]], IDlist, plotCartoon = TRUE, refShape = 'target',
outline = outline_BC0077, lines = lines_BC0077, crop = c(100,400,40,250),
flipRaster = 'y', imageList = imageList, cartoonOrder = 'under',
cartoonFill = 'black', main = 'kmeans_example')


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

summedRaster_lanRGB <- sumRaster(rasterList_lanRGB, IDlist, type = 'RGB')

plotHeat(summedRaster_lanRGB, IDlist, plotCartoon = TRUE, refShape = 'mean',
outline = outline_BC0077, lines = lines_BC0077, landList = landmarkList,
adjustCoords = TRUE, imageList = imageList, cartoonID = 'BC0077',
cartoonOrder = 'under', cartoonFill= 'black', main = 'Landmark_example')

summedRaster_lanK <- sumRaster(rasterList_lanK, IDlist, type = 'k')

plotHeat(summedRaster_lanK, IDlist, plotCartoon = TRUE, refShape = 'mean',
outline = outline_BC0077, lines = lines_BC0077, landList = landmarkList,
adjustCoords = TRUE, imageList = imageList, cartoonID = 'BC0077',
cartoonOrder = 'under', cartoonFill= 'black', main = 'Landmark_example')

plotHeat(summedRaster_lanK[[2]], IDlist, plotCartoon = TRUE, refShape = 'mean',
outline = outline_BC0077, lines = lines_BC0077, landList = landmarkList,
adjustCoords = TRUE, imageList = imageList, cartoonID = 'BC0077',
cartoonOrder = 'under', cartoonFill= 'black', main = 'Landmark_example')

## End(Not run)

StevenVB12/patternize documentation built on Nov. 2, 2023, 8:01 p.m.