Calculate Earth Mover's distance between two samples

Calculate Earth Mover's distance between two samples

Usage

EMDDist(
  x1,
  x2,
  channels = NULL,
  binSize = 0.05,
  minRange = -10,
  maxRange = 10,
  returnAll = FALSE
)

Arguments

x1

can be either a flowCore::flowFrame, or an expression matrix

x2

can be either a flowCore::flowFrame, or an expression matrix

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 x1 and x2 have been provided as flowCore::flowFrame

• if it is a numeric vector, it refers to the indexes of channels in x1

• if NULL : if x1 and x2 are provided as flowCore::flowFrames, all scatter and fluorescent channels of x1 will be selected; if x1 and x2 are provided as expression matrices, all colnames of x1 will be selected.

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 x1 and x2, which is calculated by summing up all EMD approximates for the marginal distributions of each channel

Examples

library(CytoPipeline)
#> 
#> Attaching package: ‘CytoPipeline’
#> The following objects are masked from ‘package:Biobase’:
#> 
#>     pData, pData<-

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(
    x1 = OMIP021Trans[[1]],
    x2 = OMIP021Trans[[1]])

# returning only distance, 2 channels
dist1 <- EMDDist(
    x1 = OMIP021Trans[[1]], 
    x2 = OMIP021Trans[[2]], 
    channels = c("FSC-A", "SSC-A"))

# using only one channel, passed by marker name
dist2 <- EMDDist(x1 = OMIP021Trans[[1]], 
                 x2 = OMIP021Trans[[2]], 
                 channels = c("BV785 - CD3"))

# using only one channel, passed by index
dist3 <- EMDDist(x1 = OMIP021Trans[[1]], 
                 x2 = OMIP021Trans[[2]], 
                 channels = 10)

dist2 == dist3
#> [1] TRUE