cyto_plot_layout: Set Panel Layout for cyto_plot

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

Set Panel Layout for cyto_plot

Description

cyto_plot_layout() sets the panel layout dimensions for combining different types of cyto_plot plots. Make a call to cyto_plot_layout() prior to making multiple calls to cyto_plot().

Usage

cyto_plot_layout(layout = NULL)

Arguments

layout

either a vector of the form c(nrow, ncol) defining the dimensions of the plot or a matrix defining a more sophisticated layout (see layout). Vectors can optionally contain a third element to indicate whether plots should be placed in row (1) or column (2) order, set to row order by default.

Author(s)

Dillon Hammill ([e-mail])

Examples

library(CytoExploreRData)

# Load samples into GatingSet
fs <- Activation
gs <- GatingSet(fs)

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

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

# Apply gatingTemplate
gt <- Activation_gatingTemplate
gt_gating(gt, gs)

# Set out plot layout
cyto_plot_layout(c(1,2))

# Add 2D plot
cyto_plot(gs[[4]],
  parent = "CD4 T Cells",
  alias = "",
  channels = c("Alexa Fluor 647-A", "7-AAD-A"),
  layout = FALSE
)

# Add 1D plot
cyto_plot(gs,
  parent = "CD4 T Cells",
  alias = "",
  channels = "7-AAD-A",
  density_stack = 0.6,
  layout = FALSE
)

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