matrix_raster_plot: Make a raster plot of a matrix.
In nandb: Number and Brightness Image Analysis

Description Usage Arguments Value Examples

Given a matrix mat, make a raster plot of the matrix whereby in the plot, the pixel at x = i, y = j has colour based on the value of mat[i, j] and the x axis points right and the y axis points down (see 'Details').

matrix_raster_plot(
  mat,
  scale_name = "scale",
  limits = NULL,
  ranges = NULL,
  range_names = NULL,
  colours = NULL,
  na_colour = "black",
  clip = FALSE,
  clip_low = FALSE,
  clip_high = FALSE,
  log_trans = FALSE,
  breaks = NULL,
  include_breaks = NULL
)

`mat`	The matrix you wish to plot.
`scale_name`	A string. The title of the color scale on the right of the plot.
`limits`	This gives the user the option to set all values outside a certain range to their nearest value within that range (if `clip = TRUE`) or to `NA` (if `clip = FALSE`. For example, to set all values outside the range [1.5, 2.6) to `NA`, use `limits = c(1.5, 2.6), clip = FALSE`. The colour range will cover all values within these specified limits.
`ranges`	A numeric vector. If you want specific ranges of values to have the same color, specify these ranges via an increasing numeric vector. For example, if you want the ranges 0.5-1.2 and 1.2-3, use `ranges = c(0.5, 1.2, 3)`. If `ranges` is specified as a number (a numeric vector of length 1) `n`, this is equivalent to setting ranges to be `n` equal-length intervals within the range of the matrix, i.e. it is equivalent to setting 'ranges = seq(min(mat), max(mat), length.out = n 1)`. At most one of` ranges`and`limits`should be set. If ranges is set, the behaviour for values which are not in any of the ranges are set by the`clip`arguments as in the`limits' argument.
`range_names`	A character vector. If your colour scale is discrete, here you can set the names which will label each range in the legend.
`colours`	If you have set `ranges`, here you may specify which colors you wish to colour each range. It must have the same length as the number of intervals you have specified in `ranges`. If you have not specified `ranges`, here you may specify the colours (to be passed to `ggplot2::scale_fill_gradientn()`) to create the continuous colour band. It is specified as a character vector, with the colors specified either as the values in `colors()` or as in the value of the `rgb()` function. Note that this allows the use of `grDevices::rainbow()` and friends. The default uses `viridis::viridis()`.
`na_colour`	Which colour should the `NA` pixels be? Default is black.
`clip`	If either `limits` or `ranges` are set (one should never set both), there may be values that fall outside the specified limits/ranges. If `clip = TRUE`, values outside these limits/ranges are set to their nearest values within them, but if `clip = FALSE`, these values are set to NA. Note that setting `clip = TRUE` is equivalent to setting both `clip_low` and `clip_high` to `TRUE`.
`clip_low`	Setting this to `TRUE` (and leaving `clip = FALSE`, `clip_high = FALSE`) will set all values falling below the specified limits/ranges to their nearest value within them, but all values falling above those limits/ranges will be set to `NA`.
`clip_high`	Setting this to `TRUE` (and leaving `clip = FALSE`, `clip_low = FALSE`) will set all values falling above the specified limits/ranges to their nearest value within them, but all values falling below those limits/ranges will be set to `NA`.
`log_trans`	Do you want to log-transform the colour scaling?
`breaks`	Where do you want tick marks to appear on the legend colour scale?
`include_breaks`	If you don't want to specify all the breaks, but you want some specific ones to be included on the legend colour scale, specify those specific ones here.

In the graphics console, a raster plot (via ggplot2::geom_raster()) will appear with the matrix values represented as pixel colours, with a named scale bar.

img <- ijtiff::read_tif(system.file("extdata", "50.tif", package = "nandb"))
ijtiff::display(img[, , 1, 1])
matrix_raster_plot(img[, , 1, 1])
b <- brightness(img, def = "B", detrend = FALSE, thresh = "Huang")
matrix_raster_plot(b, scale_name = "brightness")
matrix_raster_plot(b, scale_name = "brightness", log_trans = TRUE)
matrix_raster_plot(b,
  scale_name = "brightness", log_trans = TRUE,
  include_breaks = 1.35
)
matrix_raster_plot(b,
  scale_name = "brightness", log_trans = TRUE,
  breaks = 1:3
)
matrix_raster_plot(b,
  scale_name = "brightness",
  ranges = seq(0.5, 3, length.out = 6),
  range_names = paste0(1:5, "mer")
)
matrix_raster_plot(b,
  scale_name = "brightness",
  ranges = seq(0.5, 3, length.out = 6),
  range_names = paste0(1:5, "mer"), log_trans = TRUE
)
matrix_raster_plot(b,
  scale_name = "brightness",
  include_breaks = 1.25, range_names = NULL,
  log_trans = FALSE
)
matrix_raster_plot(b,
  scale_name = "brightness",
  include_breaks = 1.25, log_trans = TRUE
)
matrix_raster_plot(b,
  scale_name = "brightness",
  limits = c(1, 1.25), clip = TRUE
)
matrix_raster_plot(b,
  scale_name = "brightness",
  include_breaks = 1.25
)