cyto_plot_contour: Add contour lines to cyto_plot

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

Add contour lines to cyto_plot

Description

Add contour lines to cyto_plot

Usage

cyto_plot_contour(x, ...)

## S3 method for class 'flowFrame'
cyto_plot_contour(
  x,
  channels,
  contour_lines = 15,
  contour_line_type = 1,
  contour_line_width = 1,
  contour_line_col = "black",
  contour_line_alpha = 1,
  ...
)

## S3 method for class 'flowSet'
cyto_plot_contour(
  x,
  channels,
  contour_lines = 15,
  contour_line_type = 1,
  contour_line_width = 1,
  contour_line_col = "black",
  contour_line_alpha = 1,
  ...
)

## S3 method for class 'list'
cyto_plot_contour(
  x,
  channels,
  contour_lines = 15,
  contour_line_type = 1,
  contour_line_width = 1,
  contour_line_col = "black",
  contour_line_alpha = 1,
  ...
)

Arguments

x	either an object of class flowFrame, or flowSet or a list of flowFrame objects.
...	not in use.
channels	channels used to construct the existing cyto_plot.
contour_lines	numeric indicating the number of levels to use for contour lines, set to 15 by default.
contour_line_type	type of line to use for contour lines, set to 1 by default.
contour_line_width	line width for contour lines, set to 1 by default.
contour_line_col	colour to use for contour lines, set to "black" by default.
contour_line_alpha	numeric [0,1] to control transparency of contour lines, set to 1 by default to remove transparency.

Author(s)

Dillon Hammill, [e-mail]

Examples

library(CytoExploreRData)

# Load in Samples
fs <- Activation

# Apply compensation
fs <- cyto_compensate(fs)

# Transform fluorescent channels
trans <- cyto_transformer_logicle(fs)
fs <- cyto_transform(fs, trans)

# Plot
cyto_plot(fs[[32]],
  channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
  axes_trans = trans
)

# Contour lines
cyto_plot_contour(fs[[32]],
  channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
  contour_lines = 20
)

DillonHammill/CytoExploreR documentation built on June 8, 2025, 3:05 a.m.