plotDens: Show Density Plot of Mean Fluorescence Intensity with...

View source: R/plotDens.R

plotDensR Documentation

Show Density Plot of Mean Fluorescence Intensity with Background Cutoff

Description

Display a densityplot of each well or file with lattice graphics showing the selected background cutoff values.

Usage

plotDens(
  df,
  bgnd,
  param = "mfi",
  panel,
  adjust = 1,
  log = TRUE,
  by = NULL,
  mult = NULL,
  main = NULL,
  as.table = TRUE,
  layout = NULL,
  ...
)

Arguments

df

Annotated data.frame with imaging results.

bgnd

Numeric vector of background values. If missing, getBgnd will be called with parameters by, param, mult, and log.

param

Character string identifying the variable to be analyzed. Also passed to getBgnd if required.

panel

Optional character string defining the lattice panels, typically "well" or "file".

adjust

Numeric value controlling bandwith, passed to the density function.

log

Optional logical or numeric value to transform 'param' values. Also passed to getBgnd if required.

by, mult

Additional parameters passed to getBgnd if required.

main

Optional character string to serve as plot title. If NULL, the system date will be used.

as.table

A logical value passed to densityplot.

layout

An optional numeric vector to specify layout of densityplot, passed to densityplot.

...

Additional arguments passed to densityplot.

Details

A densityplot of image intensity in 'param' is plotted with the selected background cutoff similar to the function plotHist. Both functions can be used to examine the uniformity of results from an imaging experiment and to interactively check the paramaters passed to getBgnd to determine a suitable background cutoff value. The background values are incorporated into the strip labels.

Value

The plot is returned as an invisible lattice object.


ornelles/virustiter documentation built on March 15, 2024, 9:28 a.m.