Computation of all EMD between pairs of flowFrames belonging to a flowSet. This method provides two different input modes:
the user provides directly a flowSet loaded in memory (RAM).
the user provides (1.) a number of samples nSamples; (2.) an ad-hoc
function that takes as input an index between 1 and nSamples, and codes
the method to load the corresponding flowFrame in memory;
Optional row and column ranges can be provided to limit the calculation
to a specific rectangle of the matrix. These i.e. can be specified as a way
to split heavy calculations of large distance matrices
on several computation nodes.
pairwiseEMDDist(
x,
rowRange = c(1, nSamples),
colRange = c(min(rowRange), nSamples),
loadFlowFrameFUN = NULL,
loadFlowFrameFUNArgs = NULL,
channels = NULL,
verbose = FALSE,
BPPARAM = BiocParallel::SerialParam(),
BPOPTIONS = BiocParallel::bpoptions(packages = c("flowCore")),
binSize = 0.05,
minRange = -10,
maxRange = 10
)either a flowCore::flowSet, or the number of samples (integer >=1)
the range of rows of the distance matrix to be calculated
the range of columns of the distance matrix to be calculated
the function used to translate a flowFrame index
into a flowFrame. In other words, the function should code how to load a
specific flowFrame into memory. Important: the flow Frame index should be
the first function argument and should be named ffIndex.
(optional) a named list containing
additional input parameters of loadFlowFrameFUN()
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 fs
if NULL all scatter and fluorescent channels of fs #' will be selected
if TRUE, output a message
after each single distance calculation
sets the BPPARAM back-end to
be used for the computation. If not provided, will use
BiocParallel::SerialParam() (no task parallelization)
sets the BPOPTIONS to be
passed to bplapply() function.
Note that if you use a SnowParams back-end, you need to specify all
the packages that need to be loaded for the different CytoProcessingStep
to work properly (visibility of functions). As a minimum,
the flowCore package needs to be loaded.
(hence the default BPOPTIONS = bpoptions(packages = c("flowCore")) )
size of equal bins to approximate the marginal distributions.
minimum value taken when approximating the marginal distributions
maximum value taken when approximating the marginal distributions
a distance matrix of pairwise distances (full symmetric with 0. diagonal)
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)
# calculate pairwise distances using only FSC-A & SSC-A channels
pwDist <- pairwiseEMDDist(
x = OMIP021Trans,
channels = c("FSC-A", "SSC-A"))