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

Description Usage Arguments Value Author(s) See Also Examples

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

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

Arguments

x

a flowFrame gated in the existing plot.

gates

an object of class ellipsoidGate.

channels

a vector indicating the fluorescent channel(s) to be used for gating.

trans

object of class transformList or transformerList generated by estimateLogicle which was used to transform the fluorescent channels of the supplied flowFrame.

text

the name of the gated population, set to NA by default to only include percent in labels.

stat

indicates the type of statistic to include in the label, can be either "freq" or "count". stat is set to "freq" by default.

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.

Value

add a boxed text label to cyto_plot.

Author(s)

Dillon Hammill ([email protected])

See Also

cyto_plot_label,flowFrame,rectangleGate-method

cyto_plot_label,flowFrame,polygonGate-method

cyto_plot_label,flowFrame,list-method

cyto_plot_label,flowFrame,filters-method

Examples

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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 = "Live Cells",
  channels = c("APC-Cy7-A", "PE-A")
)

# T Cells gate
gt <- getGate(gs, "T Cells")[[1]]
cyto_plot_gate(gt,
  channels = c("APC-Cy7-A", "PE-A")
)

# Labels
cyto_plot_label(getData(gs, "Live Cells")[[4]],
  gates = gt,
  trans = trans,
  channels = c("APC-Cy7-A", "PE-A"),
  text = "T Cells",
  stat = "count",
  text_col = "magenta",
  text_size = 1.2,
  box_alpha = 1
)

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