layer_split: Split quantification in Top, Middle and Bottom

In Russel88/RCon3D: Analysis of Confocal Images of Microbial Biofilms

Split quantification in Top, Middle and Bottom

Description

Function to split quantification in Top, Middle and Bottom layer by proportion occupied

Usage

layer_split(
  qua,
  side.x,
  side.y,
  pt,
  add.t,
  add.b,
  channel = NULL,
  trim = FALSE,
  layer.start = NULL
)

Arguments

qua	A dataframe from the quant function
side.x	x dimension of image in pixels
side.y	y dimension of image in pixels
pt	The Top is defined from layer 1 (or max if layer.start="Bottom") until, but not including, the layer where the image is filled by the proportion pt (0.9 = 90 percent). If pt is set higher than found in any layer in the image then add.b specifies the Bottom and the rest is the Top. Note that if pt, add.t and add.b is set such that there is overlap between Bottom, Middle and Top, then Top will override the others
add.t	How many layers to add to the top, after pt calculation (e.g. pt=0 and add.t=10 will specify the top as the top 10 layers)
add.b	How many layers are specified as the bottom
channel	Name of channel to focus on. If NULL will aggregate all channels before splitting
trim	Should the bottom be trimmed? Specifies the bottom as the first layer (from the bottom) with max counts. Defaults to FALSE
layer.start	Are first layers the "Top" or the "Bottom" of the specimen?

Value

The original qua dataframe including an Exp variable, with a unique name for each image (based on the naming given in the quant function). And a Split varaible denoting the split

Russel88/RCon3D documentation built on Dec. 14, 2022, 11:06 p.m.