despeckle: Despeckle parameters

In beadplexr: Analysis of Multiplex Cytometric Bead Assays

Despeckle parameters

Description

Remove lonely, noisy data points in a 2D scatter matrix

Usage

despeckle(df, .parameters, .bins = 256L, .neighbours = 4L, .data = NULL, ...)

Arguments

df	A tidy data.frame.
.parameters	A character of the length of two giving the parameters to despeckle.
.bins	A numeric giving the resolution of the raster matrix. Increasing the resolution results in more isolated events.
.neighbours	A numeric giving the minimum number of neighbours. Points with fewer neighbours are removed.
.data	Deprecated. Use df.
...	Deprecated. It's use has no effect.

Details

The values of the two parameters are binned into the given number of bins. They are then cast into a 2D matrix, with the bins of the first of the parameters ending up as rows, the bins of the second parameter as columns, and combinations are marked by 1.

The rows of the df where lonely points are found in .parameters are removed.

Value

A data.frame with noisy points removed.

Examples

library(beadplexr)
library(ggplot2)

data("lplex")

lplex[[1]] |>
  ggplot() +
  aes(x = `FL6-H`, y = `FL2-H`) +
  geom_point()

lplex[[1]] |>
  despeckle(.parameters = c("FL6-H", "FL2-H"), .neighbours = 8) |>
  ggplot() +
  aes(x = `FL6-H`, y = `FL2-H`) +
  geom_point()

lplex[[1]] |>
  despeckle(.parameters = c("FL6-H", "FL2-H"), .bin = 128) |>
  ggplot() +
  aes(x = `FL6-H`, y = `FL2-H`) +
  geom_point()

beadplexr documentation built on July 9, 2023, 5:59 p.m.