Indicate Completion of Custom cyto_plot Layout for Saving

Indicate Completion of Custom cyto_plot Layout for Saving

cyto_plot_complete(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

Dillon Hammill (Dillon.Hammill@anu.edu.au)

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

# Save custom plot
cyto_plot_save("Custom.png",
  height = 8,
  width = 16
)

# 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
)

# Signal that the plot is complete
cyto_plot_complete()