Calculate Earth Mover's distance between two flowFrames

EMDDist(
  ff1,
  ff2,
  channels = NULL,
  checkChannels = TRUE,
  binSize = 0.05,
  minRange = -10,
  maxRange = 10,
  returnAll = FALSE
)

Arguments

ff1

a flowCore::flowFrame

ff2

a flowCore::flowFrame

channels

which channels (integer index(ices) or character(s)):

if it is a character vector, it can refer to either the channel names, or the marker names
if it is a numeric vector, it refers to the indexes of channels in ff1
if NULL all scatter and fluorescent channels of ff1 will be selected

checkChannels

if TRUE, will explicitly check that all provided channels are present in both flowFrames

binSize

size of equal bins to approximate the marginal distributions.

minRange

minimum value taken when approximating the marginal distributions

maxRange

maximum value taken when approximating the marginal distributions

returnAll

If TRUE, distributions and marginal distribution distances are returned as well. Default = FALSE.

Value

the Earth Mover's distance between ff1 and ff2, which is calculated by summing up all EMD approximates for the marginal distributions of each channel

Examples


library(CytoPipeline)

data(OMIP021Samples)

# estimate scale transformations 
# and transform the whole OMIP021Samples

transList <- estimateScaleTransforms(
    ff = OMIP021Samples[[1]],
    fluoMethod = "estimateLogicle",
    scatterMethod = "linearQuantile",
    scatterRefMarker = "BV785 - CD3")

OMIP021Trans <- CytoPipeline::applyScaleTransforms(
    OMIP021Samples, 
    transList)

# distance with itself (all channels at once)
# => should return 0
dist0 <- EMDDist(
    ff1 = OMIP021Trans[[1]],
    ff2 = OMIP021Trans[[1]])

# returning only distance, 2 channels
dist1 <- EMDDist(
    ff1 = OMIP021Trans[[1]], 
    ff2 = OMIP021Trans[[2]], 
    channels = c("FSC-A", "SSC-A"))

# using only one channel, passed by marker name
dist2 <- EMDDist(ff1 = OMIP021Trans[[1]], 
                    ff2 = OMIP021Trans[[2]], 
                    channels = c("BV785 - CD3"))

# using only one channel, passed by index
dist3 <- EMDDist(ff1 = OMIP021Trans[[1]], 
                    ff2 = OMIP021Trans[[2]], 
                    channels = 10)

dist2 == dist3
#> [1] TRUE