Calculate the Jensen-Shannon Divergence

Source: R/calculateJSD.R

This function calculates the Jensen-Shannon Divergence (JSD) in a SummarizedExperiment object.

# S4 method for class 'ANY'
calculateJSD(x, ...)

# S4 method for class 'SummarizedExperiment'
calculateJSD(
  x,
  assay.type = assay_name,
  assay_name = exprs_values,
  exprs_values = "counts",
  transposed = FALSE,
  ...
)

runJSD(x, BPPARAM = SerialParam(), chunkSize = nrow(x))

Arguments

x

a numeric matrix with samples as rows or a SummarizedExperiment object.

...

optional arguments not used.

assay.type

Character scalar. Specifies the name of the assay used in calculation. (Default: "counts")

assay_name

Deprecated. Use assay.type instead.

exprs_values

Deprecated. Use assay.type instead.

transposed

Logical scalar. Is x transposed with samples in rows? (Default: FALSE)

BPPARAM

A BiocParallelParam object specifying whether the calculation should be parallelized.

chunkSize

Integer scalar. Defines the size of data send to the individual worker. Only has an effect, if BPPARAM defines more than one worker. (Default: nrow(x))

Value

a sample-by-sample distance matrix, suitable for NMDS, etc.

References

Jensen-Shannon Divergence and Hilbert space embedding. Bent Fuglede and Flemming Topsoe University of Copenhagen, Department of Mathematics http://www.math.ku.dk/~topsoe/ISIT2004JSD.pdf

Author

Susan Holmes susan@stat.stanford.edu. Adapted for phyloseq by Paul J. McMurdie. Adapted for mia by Felix G.M. Ernst

Examples

data(enterotype)
library(scater)
#> Loading required package: scuttle
#> Loading required package: ggplot2


jsd <- calculateJSD(enterotype)
class(jsd)
#> [1] "dist"
head(jsd)
#> [1] 0.1282428 0.1438455 0.1001081 0.2694086 0.2413318 0.2186908

enterotype <- runMDS(enterotype, FUN = calculateJSD, name = "JSD",
                     exprs_values = "counts")
head(reducedDim(enterotype))
#>                 [,1]        [,2]
#> AM.AD.1   -0.2993825 -0.14425004
#> AM.AD.2   -0.1876141 -0.13490508
#> AM.F10.T1 -0.1761079 -0.02830419
#> AM.F10.T2 -0.1508764 -0.06346108
#> DA.AD.1   -0.2822249 -0.11871798
#> DA.AD.1T  -0.3040909 -0.11856633
head(attr(reducedDim(enterotype),"eig"))
#> [1] 12.8663937  2.9088395  1.8794319  0.8494149  0.6543775  0.5578214
attr(reducedDim(enterotype),"GOF")
#> [1] 0.5602642 0.6867101