Plot of Metric MDS object - Shepard diagram

Source: R/ggplots.R

ggplotSampleMDSShepard uses ggplot2 to provide plot of Metric MDS results. Shepard diagram provides a scatter plot of :

  • on the x axis, the high dimensional pairwise distances between each sample pairs

  • on the y axis, the corresponding pairwise distances in the obtained low dimensional projection

ggplotSampleMDSShepard(
  mdsObj,
  nDim,
  title = "Multi Dimensional Scaling - Shepard's diagram",
  pointSize = 0.5,
  lineWidth = 0.5,
  displayPseudoRSq = TRUE
)

Arguments

mdsObj

a MDS object, output of the computeMetricMDS() method.

nDim

(optional) number of dimensions to use when calculating Shepard's diagram and pseudoRSquare. If missing, it will be set equal to the number of projection dimensions as calculated in mdsObj

title

title to give to the plot

pointSize

point size in plot

lineWidth

line width in plot

displayPseudoRSq

if TRUE, display pseudo RSquare in subtitle, on top of nb of dimensions

Value

a ggplot object

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)
    
ffList <- c(
    flowCore::flowSet_to_list(OMIP021Trans),
    lapply(3:5,
           FUN = function(i) {
               aggregateAndSample(
                   OMIP021Trans,
                   seed = 10*i,
                   nTotalEvents = 5000)[,1:22]
           }))

fsNames <- c("Donor1", "Donor2", paste0("Agg",1:3))
names(ffList) <- fsNames

fsAll <- as(ffList,"flowSet")

flowCore::pData(fsAll)$type <- factor(c("real", "real", rep("synthetic", 3)))
flowCore::pData(fsAll)$grpId <- factor(c("D1", "D2", rep("Agg", 3)))

# calculate all pairwise distances

pwDist <- pairwiseEMDDist(fsAll, 
                             channels = c("FSC-A", "SSC-A"),
                             verbose = FALSE)

# compute Metric MDS object with explicit number of dimensions
mdsObj <- computeMetricMDS(pwDist, nDim = 4, seed = 0)

dim <- nDim(mdsObj) # should be 4

#' # compute Metric MDS object by reaching a target pseudo RSquare
mdsObj2 <- computeMetricMDS(pwDist, seed = 0, targetPseudoRSq = 0.999)

# Shepard diagrams 

p2D <- ggplotSampleMDSShepard(
    mdsObj,
    nDim = 2,
    pointSize = 1,
    title = "Shepard with 2 dimensions")

p3D <- ggplotSampleMDSShepard(
    mdsObj,
    nDim = 3,
    title = "Shepard with 3 dimensions") 
    #' 
pDefD <- ggplotSampleMDSShepard(
    mdsObj,
    title = "Shepard with default nb of dimensions")