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Last data update: 2014.03.03

R: Add object contours to a 'Frames' object

add.contours

R Documentation

Add object contours to a `Frames` object

Description

Creates a Frames object containing raw information, combined with the segmented images and the relative trajectory under analysis

Usage

add.contours(raw.frames, binary.frames = NULL, trajectoryset = NULL,
  trajIDs = NULL, mode = "particles", col = NULL, channel = NULL)

Arguments

`raw.frames`	A `Frames` object with raw images
`binary.frames`	A `Frames` object with preprocessed frames
`trajectoryset`	A `TrajectorySet` object
`trajIDs`	Numeric vector, the ID(s) of the trajectory.
`mode`	A character string, can assume the values `particles` or `trajectories`. Defaults to `particles`
`col`	A vector of color strings
`channel`	A character string, to select which channel to process

Details

If a TrajectorySet is provided and mode is set to trajectories, returns a Frames with all trajectories included in the IDs vector painted accordingly. If the mode is set to particles, it will just plot the particles (all) on all frames. If no TrajectorySet is provided, it will be computed with default parameters. If no binary.frames is provided, it will be computed also with default parameters

Value

A new Frames object with contours of the objects added

Author(s)

Federico Marini, marinif@uni-mainz.de, 2014

Examples

data("MesenteriumSubset")
## Not run: 
paintedTrajectories <- add.contours(raw.frames = MesenteriumSubset, mode = "trajectories",channel="red")
paintedParticles <- add.contours(raw.frames = MesenteriumSubset, mode = "particles",channel="red")
inspect.Frames(paintedTrajectories)
inspect.Frames(paintedParticles)

## End(Not run)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(flowcatchR)
Loading required package: EBImage
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowcatchR/add.contours.Rd_%03d_medium.png", width=480, height=480)
> ### Name: add.contours
> ### Title: Add object contours to a 'Frames' object
> ### Aliases: add.contours
> 
> ### ** Examples
> 
> data("MesenteriumSubset")
> ## Not run: 
> ##D paintedTrajectories <- add.contours(raw.frames = MesenteriumSubset, mode = "trajectories",channel="red")
> ##D paintedParticles <- add.contours(raw.frames = MesenteriumSubset, mode = "particles",channel="red")
> ##D inspect.Frames(paintedTrajectories)
> ##D inspect.Frames(paintedParticles)
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

Add object contours to a Frames object