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plot filtered events in 2D, using ggplot

Source: R/ggplots.R
ggplotFilterEvents.Rd

plot events of specific channels of either : flowCore::flowFrame, or flowCore::flowSet in 2D, showing the impact of applying a filter between :

  • a 'pre' flowframe

Usage

ggplotFilterEvents(
  ffPre,
  ffPost,
  xChannel,
  yChannel,
  nDisplayCells = 10000,
  seed = NULL,
  size = 0.5,
  xScale = c("linear", "logicle"),
  yScale = c("linear", "logicle"),
  xLogicleParams = NULL,
  yLogicleParams = NULL,
  xLinearRange = NULL,
  yLinearRange = NULL,
  transList = NULL,
  runTransforms = FALSE,
  interactive = FALSE
)

Arguments

ffPre

a flowCore::flowFrame, before applying filter

ffPost

a flowCore::flowFrame, after applying filter

xChannel

channel (name or index) or marker name to be displayed on x axis

yChannel

channel (name or index) or marker name to be displayed on y axis

nDisplayCells

maximum number of events that will be plotted. If the number of events exceed this number, a subsampling will be performed

seed

seed used for sub-sampling (if any)

size

used by geom_point()

xScale

scale to be used for the x axis (note "linear" corresponds to no transformation)

yScale

scale to be used for the y axis (note "linear" corresponds to no transformation)

xLogicleParams

if (xScale == "logicle"), the parameters of the logicle transformation to be used, as a list(w = ..., m = ..., a = ..., t = ...) If NULL, these parameters will be estimated by flowCore::estimateLogicle()

yLogicleParams

if (yScale == "logicle"), the parameters of the logicle transformation to be used, as a list(w = ..., m = ..., a = ..., t = ...) If NULL, these parameters will be estimated by flowCore::estimateLogicle()

xLinearRange

if (xScale == "linear"), linear range to be used

yLinearRange

if (yScale == "linear"), linear range to be used

transList

optional list of scale transformations to be applied to each channel. If it is non null, 'x/yScale', 'x/yLogicleParams' and 'x/yLinear_range' will be discarded.

runTransforms

(TRUE/FALSE) Will the application of non linear scale result in data being effectively transformed ?

  • If TRUE, than the data will undergo transformations prior to visualization.

  • If FALSE, the axis will be scaled but the data themselves are not transformed.

interactive

if TRUE, transform the scaling formats such that the ggcyto::x_scale_logicle() and ggcyto::y_scale_logicle() do work with plotly::ggplotly()

Value

a ggplot object

Examples


data(OMIP021Samples)

ffPre <- OMIP021Samples[[1]]

# creating a manual polygon gate filter based on channels L/D and FSC-A

LDMarker <- "L/D Aqua - Viability"

LDChannel <- getChannelNamesFromMarkers(ffPre, markers = LDMarker)
liveGateMatrix <- matrix(
    data = c(
        50000, 50000, 100000, 200000, 200000,
        100, 1000, 2000, 2000, 1
    ),
    ncol = 2,
    dimnames = list(
        c(),
        c("FSC-A", LDChannel)
    )
)

liveGate <- flowCore::polygonGate(
    filterId = "Live",
    .gate = liveGateMatrix
)

selectedLive <- flowCore::filter(ffPre, liveGate)
ffL <- flowCore::Subset(ffPre, selectedLive)


# show the results

# subsample 5000 points    
ggplotFilterEvents(
    ffPre = ffPre,
    ffPost = ffL,
    nDisplayCells = 5000,
    xChannel = "FSC-A", xScale = "linear",
    yChannel = LDMarker, yScale = "logicle") +
    ggplot2::ggtitle("Live gate filter - 5000 points")
#> Warning: Removed 3 rows containing missing values or values outside the scale range
#> (`geom_point()`).


# with all points
ggplotFilterEvents(
    ffPre = ffPre,
    ffPost = ffL,
    nDisplayCells = Inf,
    xChannel = "FSC-A", xScale = "linear",
    yChannel = LDMarker, yScale = "logicle") +
    ggplot2::ggtitle("Live gate filter - all points")
#> Warning: Removed 3 rows containing missing values or values outside the scale range
#> (`geom_point()`).