cyto_plot_label-flowFrame-rectangleGate-method: Add boxed text labels to cyto_plot - rectangleGate Method

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

Description

cyto_plot_label takes on a flowFrame object, population name text, channels and a gate object to construct a text label for the plot with the population name and frequency.

Usage

## S4 method for signature 'flowFrame,rectangleGate'
cyto_plot_label(x, gates = NULL,
  trans = NULL, channels, text = NA, stat = NA, text_x = NA,
  text_y = NA, text_font = 2, text_size = 0.8, text_col = "black",
  box_alpha = 0.6, density_smooth = 1.5)

Arguments

x	a flowFrame gated in the existing plot.
gates	an object of class rectangleGate.
trans	object of class transformList or transformerList generated by estimateLogicle which was used to transform the fluorescent channels of the supplied flowFrame.
channels	a vector indicating the fluorescent channel(s) to be used for gating.
text	character string to include in the label above the statistic (e.g. population name(s)).
stat	indicates the type of statistic to include in the label, can be either "freq", "count", "median", "mean", "mode", "geo mean" or "CV". stat is set to "freq" by default. Statistics for fluorescent intensity are calculated for the entire distribution. Only count and percent statistics are supported for 2D plots.
text_x	vector containing the x co-ordinates for the plot labels. Set to NULL by default to place labels in the center of the gates.
text_y	vector containing the x co-ordinates for the plot labels. Set to NULL by default to place labels in the center of the gates.
text_font	integer [1,2,3,4] passed to text to alter the font, set to 2 by default for a bold font.
text_size	numeric character expansion used to control the size of the text in the labels, set to 0.8 by default. See ?text for details.
text_col	specify text colour in label for each gate, defaults to "black" for all gates.
box_alpha	numeric [0,1] controls the transparency of the background, set to 0.6 by default.
density_smooth	smoothing parameter passed to density to adjust kernel density for mode calculation.

Value

add a boxed text label to cyto_plot.

Author(s)

Dillon Hammill ([e-mail])

See Also

cyto_plot_label,flowFrame,polygonGate-method

cyto_plot_label,flowFrame,ellipsoidGate-method

cyto_plot_label,flowFrame,list-method

cyto_plot_label,flowFrame,filters-method

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(fs))
gs <- transform(gs, trans)

# Gate using gate_draw
gating(Activation_gatingTemplate, gs)

# Plot
cyto_plot(gs[[4]],
  parent = "CD4 T Cells",
  channels = "7-AAD-A"
)

# CD69+ CD4 T Cells gate
gt <- getGate(gs, "CD69+ CD4 T Cells")[[1]]
cyto_plot_gate(gt,
  channels = "7-AAD-A"
)

# Labels
cyto_plot_label(getData(gs, "CD4 T Cells")[[4]],
  gates = gt,
  trans = trans,
  channels = "7-AAD-A",
  text = c("CD69+"),
  stat = "freq",
  text_col = "blue"
)

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