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Plot filtered element-wise average and differences for two cartridge case scans

x3p_comparisonPlot.Rd

Plot filtered element-wise average and differences for two cartridge case scans

Usage

x3p_comparisonPlot(
  x3p1,
  x3p2,
  threshold = 1,
  plotLabels = c("x3p1", "x3p2", "Element-wise Average", "x3p1 diff.", "x3p2 diff."),
  showOutlines = TRUE,
  labelSize = 4,
  label_x = ncol(x3p1$surface.matrix)/2,
  label_y = nrow(x3p1$surface.matrix)/2,
  type = "faceted",
  legendLength = grid::unit(3, "in"),
  legendUnit = "Norm.",
  legendHoriz = -1.2,
  legendQuantiles = c(0, 0.01, 0.25, 0.5, 0.75, 0.99, 1)
)

Arguments

x3p1

an x3p object

x3p2

another x3p object

threshold

the default filtering threshold. Defaults to a scalar (1 micron = 1e-6 meters), but can also be set to a scalar-valued function that takes x3p1 and x3p2 as arguments. For example, threshold = impressions::x3p_sd will use the joint standard deviation of x3p1 and x3p2 as the threshold.

plotLabels

a character vector of five elements that will display as labels on each plot

showOutlines

boolean value of whether to show outline around the filtered elements in the element-wise average and difference plots. See notes for more details

labelSize

font size for the plot labels

label_x

horizontal location of the plot labels

label_y

vertical location of the plot labels

type

return the five plots in a single, faceted plot or as a list

legendLength

length of the plot legend. Passed to the barwidth argument of the ggplot2::guide_colorbar function

legendUnit

unit of measurement for the surface values (typically either "micron" or "Norm.")

legendHoriz

horizontal location of the legend. Passed to the patchwork::inset_element function

legendQuantiles

quantile values to be shown as legend labels. Passed within the breaks argument of the ggplot2::scale_fill_gradientn function

Note

The showOutlines argument set to FALSE sidesteps a computation of outlines for the filtered regions in the comparison plot. This is because some systems, particularly Linux systems, may not have the necessary libraries required to compute the outline installed by default. Specifically, the function to compute the outlines relies on an R package called rgeos (https://cran.r-project.org/web/packages/rgeos/index.html), which is an API to the geos geometry engine (https://libgeos.org/). Linux users need to install geos to install rgeos to compute the outline. See this post for more info: https://stackoverflow.com/questions/53389181/installing-the-r-package-rgeos-on-linux-geos-config-not-found-or-not-executab Alternatively, you can skip the outline calculation all together using this showOutlines argument at the expense of not seeing the region outlines, which are more a nice visual aid than a necessary component of the plot.

See also

dplyr::guide_colorbar

Examples

data("K013sA1","K013sA2")

compData <- cmcR::comparison_allTogether(reference = K013sA1,
                                         target = K013sA2,
                                         theta = 3,numCells = c(1,1),
                                         maxMissingProp = .99,
                                         sideLengthMultiplier = 1.1,
                                         returnX3Ps = TRUE)

x3p_comparisonPlot(x3p1 = compData$cellHeightValues[[1]],x3p2 = compData$alignedTargetCell[[1]])
#> Regions defined for each Polygons
#> Warning: Duplicated aesthetics after name standardisation: colour
#> Warning: Duplicated aesthetics after name standardisation: colour
#> Warning: Duplicated aesthetics after name standardisation: colour
#> Warning: Raster pixels are placed at uneven horizontal intervals and will be shifted
#> ℹ Consider using `geom_tile()` instead.
#> Warning: Raster pixels are placed at uneven horizontal intervals and will be shifted
#> ℹ Consider using `geom_tile()` instead.
#> Warning: Raster pixels are placed at uneven horizontal intervals and will be shifted
#> ℹ Consider using `geom_tile()` instead.
#> Warning: Raster pixels are placed at uneven horizontal intervals and will be shifted
#> ℹ Consider using `geom_tile()` instead.