rubitPlotHeatmap: Plot a 2D density estimate of all areas.

In JoGall/rubitrail: rubitrail, a package to analyse the output of UbiTrail, an open-source video tracking program for analysis of animal locomotion.

Description

This function represents the relative position density of each agent during the entire experiment.

Usage

rubitPlotHeatmap(l, refImg = NA, resol = 50, h = 10,
  palet = rubitTransCol(50, 0.5))

Arguments

l	a list of area matrices returned by rubitLoadFile or rubitBasic.
refImg	the path to a reference TIFF image (see details).
resol	the resolution of the kernel density estimate.
h	the bandwidth ratio (see details).
palet	a vector of colours.

Note

The list l can be obtained by rubitBasic. refImg is an image of the same size as the video frames. If specified (i.e. if refImg != NA), the function will use the image as background for the plot. An easy way to obtain such an image is to ask UbiTrail to save the first frame (by ticking the corresponding box in the GUI). For each area, the kernel estimate density function will use a bandwidth bw = W/h, where W is the width of the area.

See Also

rubitLinearInterpolate for interpolating data. MASS::kde2d is used by this function.

Examples

data(tenebrio_basic)

rubitPlotHeatmap(tenebrio_basic)
rubitPlotHeatmap(tenebrio_basic, resol=150)

JoGall/rubitrail documentation built on May 7, 2019, 10:53 a.m.