Plot rectangleGate Objects onto an Existing plot

Plot rectangleGate Objects onto an Existing plot

# S4 method for rectangleGate
cyto_plot_gate(x, channels, gate_line_type = 1,
  gate_line_width = 2.5, gate_line_col = "red", gate_point = FALSE,
  gate_point_shape = 16, gate_point_size = 1)

Arguments

x	an object of class rectangleGate.
channels	fluorescent channels to used to construct the plot.
gate_line_type	integer [0,6] which controls the line type, set to 1 to draw solid lines by default.
gate_line_width	numeric to adjust line thickness of gates, set to 2.5 by default.
gate_line_col	indicates the colour of the gate to be constructed, set to "red" by default.
gate_point	logical indicating whether points should be included when plotting the gates, set to FALSE by default.
gate_point_shape	integer [0,25] passed to pch to control the shape of the points, set to 16 to draw filled circles by default. For other shapes refer to ?pch.
gate_point_size	numeric character expansion to control the size of the points in the drawn gate, set to 1 by default.

Value

gate object with modified co-ordinates for plotting.

See also

cyto_plot_gate,polygonGate-method

cyto_plot_gate,ellipsoidGate-method

cyto_plot_gate,list-method

cyto_plot_gate,filters-method

Examples

library(CytoRSuiteData)

# Load in samples
fs <- Activation
gs <- GatingSet(fs)
#> .
#> .
#> .
#> .
#> done!

# 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)
#> Preprocessing for 'Cells'
#> Gating for 'Cells'
#> done.
#> Preprocessing for 'Single Cells'
#> Gating for 'Single Cells'
#> done.
#> Preprocessing for 'Live Cells'
#> Gating for 'Live Cells'
#> done.
#> Preprocessing for 'Dendritic Cells'
#> Gating for 'Dendritic Cells'
#> done.
#> Preprocessing for 'T Cells'
#> Gating for 'T Cells'
#> done.
#> Preprocessing for 'CD8 T Cells'
#> Gating for 'CD8 T Cells'
#> done.
#> Preprocessing for 'CD69+ CD8 T Cells'
#> Gating for 'CD69+ CD8 T Cells'
#> done.
#> Preprocessing for 'CD4 T Cells'
#> Gating for 'CD4 T Cells'
#> done.
#> Preprocessing for 'CD69+ CD4 T Cells'
#> Gating for 'CD69+ CD4 T Cells'
#> done.
#> finished.

# Plot
cyto_plot(gs[[4]],
  parent = "T Cells",
  channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
  axes_trans = trans
)

# CD4 T Cells gate
cyto_plot_gate(getGate(gs, "CD4 T Cells")[[1]],
  channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
  gate_line_col = "purple"
)