Plot of Metric MDS object

ggplotSampleMDS uses ggplot2 to provide plots of Metric MDS results. By default, a pseudo Rsquare projection quality indicator, and the number of dimensions of the MDS projection are provided in sub-title

Usage

ggplotSampleMDS(
  mdsObj,
  pData,
  sampleSubset,
  projectionAxes = c(1, 2),
  biplot = FALSE,
  biplotType = c("correlation", "regression"),
  extVariables,
  pDataForColour,
  pDataForShape,
  pDataForLabel,
  pDataForAdditionalLabelling,
  pointSize = 1,
  pointSizeReflectingStress = FALSE,
  title = "Multi Dimensional Scaling",
  displayPointLabels = TRUE,
  pointLabelSize = 3.88,
  repelPointLabels = TRUE,
  displayArrowLabels = TRUE,
  arrowLabelSize = 3.88,
  repelArrowLabels = FALSE,
  arrowThreshold = 0.8,
  flipXAxis = FALSE,
  flipYAxis = FALSE,
  displayPseudoRSq = TRUE,
  ...
)

Arguments

mdsObj

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

pData

(optional) a data.frame providing user input sample data. These can be design of experiment variables, phenotype data per sample,... and will be used to highlight sample categories in the plot and/or for subsetting.

sampleSubset

(optional) a logical vector, of size nrow(pData), which is by construction the nb of samples, indicating which samples to keep in the plot. Typically it is obtained through the evaluation of a logical condition on pData rows.

projectionAxes

which two axes should be plotted (should be a numeric vector of length 2)

biplot

if TRUE, adds projection of external variables

biplotType

type of biplot used:

if "correlation", projection of external variables will be according to Pearson correlations w.r.t. projection axes (arrow x & y coordinates)
if "regression", a linear regression of external variables using the 2 projection axes as explanatory variables is performed, and the projection of external variables will be according to regression coefficients (arrow direction) and R square of regression (arrow size)

extVariables

are used to generate a biplot these are the external variables that will be used in the biplot. They should be provided as a matrix with named columns corresponding to the variables. The number of rows should be the same as the number of samples. The matrix might contain some NA's, in that case only complete rows will be used to calculate biplot arrows.

pDataForColour

(optional) which pData variable will be used as colour aesthetic. Should be a character.

pDataForShape

(optional) which pData variable will be used as shape aesthetic. Should be a character.

pDataForLabel

(optional) which pData variable will be used as point labels in the plot. Should be a character. If missing, point labels will be set equal to point names defined in MDS object (if not NULL, otherwise no labels will be set).

pDataForAdditionalLabelling

(optional) which pData variable(s) will be add to the ggplot mapping, as to make them available for plotly tooltipping. Should be an array of character of maximum length 3. Note this works only if biplot=FALSE, as biplots contain circle and arrows that are currently not supported under ggplotly.

pointSize

size of all points on the plots - only when pointSizeReflectingStress is FALSE.

pointSizeReflectingStress

if TRUE, size of points will appear proportional to stress by point, i.e. the bigger the sample point appears, the less accurate its representation is (in terms of distances w.r.t. other points)

title

title to give to the plot

displayPointLabels

if TRUE, displays labels attached to points (see pDataForLabels for the setting of the label values)

pointLabelSize

size of point labels (default: 3.88 as in geom_text())

repelPointLabels

if TRUE, uses ggrepel::geom_text_repel() instead of ggplot2::geom_text() (try to split the labels such that they do not overlap) for the points

displayArrowLabels

if TRUE, displays arrows labels (only with biplot)

arrowLabelSize

size of arrow labels (default: 3.88 as in geom_text())

repelArrowLabels

if TRUE, uses ggrepel::geom_text_repel() instead of ggplot2::geom_text() for the arrows (only with biplot)

arrowThreshold

(only with biplot), arrows will be made barely visible if their length is (in absolute value) less than this threshold.

flipXAxis

if TRUE, take the opposite of x values (provided as it might ease low dimensional projection comparisons)

flipYAxis

if TRUE, take the opposite of y values (provided as it might ease low dimensional projection comparisons)

displayPseudoRSq

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

...

additional parameters passed to ggrepel::geom_text_repel() (if used)

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)

# As there are only 2 samples in OMIP021Samples dataset,
# we create artificial samples that are random combinations of both samples

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)



# plot mds projection on axes 1 and 2,
# use 'grpId' for colour, 'type' for shape, and no label 

p_12 <- ggplotSampleMDS(
    mdsObj = mdsObj,
    pData = flowCore::pData(fsAll),
    projectionAxes = c(1,2),
    pDataForColour = "grpId",
    pDataForShape = "type")

# plot mds projection on axes 3 and 4,
# use 'grpId' for colour, and 'name' as point label

p_34 <- ggplotSampleMDS(
    mdsObj = mdsObj,
    pData = flowCore::pData(fsAll),
    projectionAxes = c(3,4),
    pDataForColour = "grpId",
    pDataForLabel = "name")

# plot mds projection on axes 1 and 2,
# use 'group' for colour, 'type' for shape, and 'name' as point label
# have sample point size reflecting 'stress'
# i.e. quality of projection w.r.t. distances to other points

p12_Stress <- ggplotSampleMDS(
    mdsObj = mdsObj,
    pData = flowCore::pData(fsAll),
    projectionAxes = c(1,2),
    pDataForColour = "grpId",
    pDataForLabel = "name",
    pDataForShape = "type",
    pointSizeReflectingStress = TRUE)

# try to associate axes with median of each channel
# => use bi-plot

extVars <- channelSummaryStats(
    fsAll,
    channels = c("FSC-A", "SSC-A"),
    statFUNs = stats::median)


bp_12 <- ggplotSampleMDS(
    mdsObj = mdsObj,
    pData = flowCore::pData(fsAll),
    projectionAxes = c(1,2),
    biplot = TRUE,
    extVariables = extVars,
    pDataForColour = "grpId",
    pDataForShape = "type",
    seed = 0)

bp_34 <- ggplotSampleMDS(
    mdsObj = mdsObj,
    pData = flowCore::pData(fsAll),
    projectionAxes = c(3,4),
    biplot = TRUE,
    extVariables = extVars,
    pDataForColour = "grpId",
    pDataForLabel = "name",
    seed = 0)

Usage

Arguments

Value

See also

Examples