cyto_plot_overlay-flowSet-method: Overlay Points on cyto_plot - flowSet Method

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

Description

Overlay Points on cyto_plot - flowSet Method

Usage

## S4 method for signature 'flowSet'
cyto_plot_overlay(x, channels, point_shape = ".",
  point_size = 2, point_col = "black", point_alpha = 1)

Arguments

x	object of class flowSet to overlay onto an existing cyto_plot.
channels	channels used to construct the existing cyto_plot.
point_shape	point character to use for points, set to "." by default to maximise plotting speed.
point_size	numeric specifying the degree of character expansion for points, set to 2 by default.
point_col	colours to use for points, set to "black" by default.
point_alpha	numeric [0,1] used to control colour transparency, set to 1 by default to remove transparency.

Author(s)

Dillon Hammill, [e-mail]

Examples

library(CytoRSuiteData)

# Load in samples
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)

# Gate using gate_draw
gating(Activation_gatingTemplate, gs)

# Plot
cyto_plot(gs[[4]],
  parent = "Live Cells",
  channels = c("APC-Cy7-A", "PE-A"),
  axes_trans = trans
)

# Overlay CD4 T Cells
cyto_plot_overlay(getData(gs, "CD4 T Cells")[2:4],
  channels = c("APC-Cy7-A", "PE-A"),
  point_col = c("magenta", "orange", "green")
)

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