calib.plot: Diagnostic tool for looking at calibration images and the...

In J0vid/Colormesh: Functions for Processing Image Color Data for Statistical Analysis

Description

Diagnostic tool for looking at calibration images and the sampling landmarks

Usage

calib.plot(
  imagedir,
  image.names,
  calib.file,
  cex = 2,
  col = "red",
  individual = 1,
  flip.y.values = F
)

Arguments

imagedir	path to calibration images
image.names	A vector of image names to look for in imagedir.
calib.file	tps2array object with the sampled color standard. Make sure the IMAGE data in the tps file matches the names of the images exactly. It's okay if it still has a path attached to the name.
cex	change the point size on the image
col	change point colors
individual	which specimen do you want to plot? Defaults to the first specimen
flip.y.values	logical value to try flipping the Y values of the coordinates to see if the landmarks will match up with the color standard

Value

a plot to check if you should flip the y-axis of the color standard landmarks

Examples

#load covariates and calibration file
specimen.factors <- read.csv(system.file("extdata", "specimen_factors.csv", package = "Colormesh"), header = F)
calib.file <- tps2array(system.file("extdata", "calib_LM_coords.TPS", package = "Colormesh"))

calib.plot(paste0(path.package("Colormesh"),"/extdata/original_images/"), image.names = specimen.factors[,1], calib.file = calib.file)

J0vid/Colormesh documentation built on Feb. 4, 2022, 1:33 a.m.