savePlotCollEvents2D: Save plots of collective events in 2D
In dmattek/ARCOS: Automatic Recognition of Collective Signalling

savePlotCollEvents2D

R Documentation

Save plots of collective events in 2D

Description

Save subsequent frames as PNG or PDF files with optional collective events overlaid as convex hull polygons over the original data. Optionally, a binarised measurement can be plotted as black dots and arbitrary annotations as asterisks.

Usage

savePlotCollEvents2D(
  inDTobj,
  inDTcoll = NULL,
  inDTbin = NULL,
  inDTanno = NULL,
  inCols = list(frame = "frame", x = "x", y = "y", id = "trackID", clid = "clTrackID", m
    = "m", mb = "mb"),
  inDirPath = ".",
  inFileCore = "",
  inXlim = c(0, 1024),
  inYlim = c(0, 1024),
  inPlotWH = c(3, 3),
  inRevY = TRUE,
  inStretchF = TRUE,
  inPtSzMain = 2,
  inPtSzBin = 1,
  inPtSzAnno = 2,
  inGGtheme = NULL,
  inPlotType = c("png", "pdf"),
  inColPal = "RdYlBu"
)

Arguments

`inDTobj`	a data.table with time series in long format; required.
`inDTcoll`	a data.table with collective events in long format; e.g. created by trackCollEvents; default NULL.
`inDTbin`	a data.table with a binarised measurement to plot as black dots; default NULL.
`inDTanno`	a data.table with annotations to plot as asterisks.
`inCols`	a list with column names, default list(frame = "frame", x = "x", y = "y", id = "trackID", clid = "clTrackID", m = "m", mb = "mb").
`inDirPath`	a string with the path to save output images, default ".".
`inFileCore`	a string with a prefix for output image files, default ".".
`inXlim`	a vector with limits for the x-axis, default c(0, 1024).
`inYlim`	a vector with limits for the y-axis, default c(0, 1024).
`inPlotWH`	a vector with width and height of the output image in inches, default c(3,3).
`inRevY`	logical, whether to reverse the y-axis, default TRUE.
`inStretchF`	logical, whether to stretch the output sequence to include frames without objects, default TRUE.
`inPtSzMain`	numeric, size of main points, default 1.
`inPtSzBin`	numeric, size of points that indicate binarised measurement, default 0.1.
`inPtSzAnno`	numeric, size of points that indicate annotated data, default 2.
`inGGtheme`	additional ggplot2 theme definitions, default NULL.
`inPlotType`	definition of the output image type, either "png" or "pdf".
`inColPal`	colour palette for the main data, default 'RdYlBu'.