colordistance (version 1.1.2)

getColorDistanceMatrix: Distance matrix for a list of color cluster sets

Description

Calculates a distance matrix for a list of color cluster sets as returned by extractClusters or getHistList based on the specified distance metric.

Usage

getColorDistanceMatrix(
  cluster.list,
  method = "emd",
  ordering = "default",
  size.weight = 0.5,
  color.weight = 0.5,
  plotting = TRUE,
  ...
)

Arguments

cluster.list

A list of identically sized dataframes with 4 columns each (R, G, B, Pct or H, S, V, Pct) as output by extractClusters or getHistList.

method

One of four possible comparison methods for calculating the color distances: "emd" (uses EMDistance, recommended), "chisq" (uses chisqDistance), "color.dist" (uses colorDistance; not appropriate if binAvg=F), or "weighted.pairs" (weightedPairsDistance).

ordering

Logical if not left as "default". Should the color clusters in the list be reordered to minimize the distances between the pairs? If left as default, ordering depends on distance method: "emd" and "chisq" do not order clusters ("emd" orders on a case-by-case in the EMDistance function itself and reordering by size similarity would make chi-squared meaningless); "color.dist" and "weighted.pairs" use ordering. To override defaults, set to either T (for ordering) or F (for no ordering).

size.weight

Same as in weightedPairsDistance.

color.weight

Same as in weightedPairsDistance.

plotting

Logical. Should a heatmap of the distance matrix be displayed once the function finishes running?

...

Additional arguments passed on to heatmapColorDistance.

Value

A distance matrix of image distance scores (the scales vary depending on the distance metric chosen, but for all four methods, higher scores = more different).

Details

Each cell represents the distance between a pair of color cluster sets as measured using either chi-squared distance (cluster size only), earth mover's distance (size and color), weighted pairs (size and color with user-specified weights for each), or color distance (Euclidean distance between clusters as 3-dimensional - RGB or HSV - color coordinates).

Earth mover's distance is recommended unless binAvg is set to false during cluster list generation (in which case all paired bins will have the same colors across datasets), in which case chi-squared is recommended. Weighted pairs or color distance may be appropriate depending on the question, but generally give poorer results.

Examples

# NOT RUN {
cluster.list <- colordistance::getHistList(c(system.file("extdata",
"Heliconius/Heliconius_A", package="colordistance"), system.file("extdata",
"Heliconius/Heliconius_B", package="colordistance")), lower=rep(0.8, 3),
upper=rep(1, 3))

# Default values - recommended!
colordistance::getColorDistanceMatrix(cluster.list, main="EMD")

# Without plotting
colordistance::getColorDistanceMatrix(cluster.list, plotting=FALSE)

# Use chi-squared instead
colordistance::getColorDistanceMatrix(cluster.list, method="chisq", main="Chi-squared")

# Override ordering (throws a warning if you're trying to do this with
# chisq!)
colordistance::getColorDistanceMatrix(cluster.list, method="chisq",
ordering=TRUE, main="Chi-squared w/ ordering")

# Specify high size weight/low color weight for weighted pairs
colordistance::getColorDistanceMatrix(cluster.list, method="weighted.pairs",
color.weight=0.1, size.weight=0.9, main="Weighted pairs")

# Color distance only
colordistance::getColorDistanceMatrix(cluster.list, method="color.dist",
ordering=TRUE, main="Color distance only")
# }