clumps_plot: Plot 3D aggregates
In Russel88/RCon3D: Analysis of Confocal Images of Microbial Biofilms

clumps_plot

R Documentation

Plot 3D aggregates

Description

Provide pwidth and zstep to get true aspect ratio. Provide center and radius to draw a circular outline

Usage

clumps_plot(
  clumps.out,
  replica = 1,
  col = "agg",
  pwidth = NULL,
  zstep = NULL,
  center = NULL,
  radius = NULL,
  thresh = 0,
  thresh.m = FALSE
)

Arguments

`clumps.out`	Output from `clumps`
`replica`	Image replica to plot
`col`	Colour by aggregate ID ("agg") or by distance to a point ("dist")
`pwidth`	Pixel width in microns
`zstep`	Microns between the layers
`center`	3D coordinates (c(x,y,z)) of where to center circular outline
`radius`	Radius of the circular outline, in microns if pwidth and zstep are provided, else in pixels
`thresh`	Clumps smaller than this are not plotted (in pixels)
`thresh.m`	If TRUE will apply threshold to sizes in microns instead of pixels