plotTrackMeasures {celltrackR}

Bivariate Scatterplot of Track Measures

Description

Plots the values of two measures applied on the given tracks against each other.

Usage

plotTrackMeasures(
  x,
  measure.x,
  measure.y,
  add = FALSE,
  xlab = deparse(substitute(measure.x)),
  ylab = deparse(substitute(measure.y)),
  ellipse.col = "red",
  ellipse.border = "black",
  conf.level = 0.95,
  ...
)

Arguments

x

the input tracks object.

measure.x

the measure to be shown on the X axis (see TrackMeasures).

measure.y

the measure to be shown on the Y axis.

add

a logical indicating whether the tracks are to be added to an existing plot via points.

xlab

label of the x-axis. By default the name of the input function measure.x.

ylab

label of the y-axis. By default the name of the input function measure.y.

ellipse.col

color with which to draw the confidence ellipse of the mean (for 1D, this corresponds to the confidence interval of the mean). Use NA to omit the confidence ellipse.

ellipse.border

color of the confidence ellipse border. Use NA to omit the border.

conf.level

the desired confidence level for the confidence ellipse.

...

additional parameters to be passed to plot (in case add=FALSE) or points (add=TRUE).

Details

Plots the value of measurey applied to x against the value of measurey applied to y. This is useful for "FACS-like" motility analysis, where clusters of cell tracks are identified based on their motility parameters (Moreau et al, 2012; Textor et al, 2014).

Value

None

References

Moreau HD, Lemaitre F, Terriac E, Azar G, Piel M, Lennon-Dumenil AM, Bousso P (2012), Dynamic In Situ Cytometry Uncovers T Cell Receptor Signaling during Immunological Synapses and Kinapses In Vivo. Immunity 37(2), 351–363. doi:10.1016/j.immuni.2012.05.014

Johannes Textor, Sarah E. Henrickson, Judith N. Mandl, Ulrich H. von Andrian, J\"urgen Westermann, Rob J. de Boer and Joost B. Beltman (2014), Random Migration and Signal Integration Promote Rapid and Robust T Cell Recruitment. PLoS Computational Biology 10(8), e1003752. doi:10.1371/journal.pcbi.1003752

Examples

## Compare speed and straightness of 3 example population tracks.
## To make the comparison fair, analyze subtracks of fixed length.
plotTrackMeasures( subtracks(TCells,4,0), speed, straightness, ellipse.col="black" )
plotTrackMeasures( subtracks(BCells,4,0), speed, straightness,
  col=2, ellipse.col=2, pch=2, add=TRUE )
plotTrackMeasures( subtracks(Neutrophils,4,0), speed, straightness,
  col=3, ellipse.col=3, pch=3, add=TRUE )