cyto_plot_contour-list-method: Contour Lines for cyto_plot - list Method

In DillonHammill/cytoSuite: Compensation, Gating & Visualisation Toolkit for Analysis of Flow Cytometry Data

Description

Contour Lines for cyto_plot - list Method

Usage

## S4 method for signature 'list'
cyto_plot_contour(x, channels, contour_lines = 15,
  contour_line_type = 1, contour_line_width = 1,
  contour_line_col = "black")

Arguments

x	a list of flowFrame objects to use for contour lines to overlay onto an existing cyto_plot.
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 2 by default.
contour_line_col	colour to use for contour lines, set to "black" by default.

Author(s)

Dillon Hammill, [e-mail]

Examples

library(CytoRSuiteData)

# Load in Samples
fs <- Activation

# Apply compensation
fs <- compensate(fs, fs[[1]]@description$SPILL)

# Transform fluorescent channels
trans <- estimateLogicle(fs[[4]], cyto_fluor_channels(fs))
fs <- transform(fs, trans)

# Plot
cyto_plot(fs,
  channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
  group_by = "all", axes_trans = trans
)

# Contour lines for control sample
cyto_plot_contour(list(fs[[1]], fs[[2]], fs[[3]], fs[[4]]),
  channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
  contour_lines = c(20, 0, 0, 0)
)

DillonHammill/cytoSuite documentation built on March 7, 2019, 10:09 a.m.